Starting phenix.real_space_refine on Wed Sep 17 14:55:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7d_61202/09_2025/9j7d_61202_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7d_61202/09_2025/9j7d_61202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j7d_61202/09_2025/9j7d_61202_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7d_61202/09_2025/9j7d_61202_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j7d_61202/09_2025/9j7d_61202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7d_61202/09_2025/9j7d_61202.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6138 2.51 5 N 1474 2.21 5 O 1570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9222 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4516 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 19, 'TRANS': 577} Chain breaks: 3 Chain: "B" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4516 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 19, 'TRANS': 577} Chain breaks: 3 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {'C14': 1, 'R16': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'R16': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.50, per 1000 atoms: 0.27 Number of scatterers: 9222 At special positions: 0 Unit cell: (118.15, 87.55, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1570 8.00 N 1474 7.00 C 6138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 275 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 410.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 80.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 removed outlier: 3.620A pdb=" N TYR A 13 " --> pdb=" O SER A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 61 removed outlier: 3.595A pdb=" N GLY A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 removed outlier: 3.507A pdb=" N GLN A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 removed outlier: 4.482A pdb=" N SER A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 removed outlier: 4.327A pdb=" N PHE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 137 removed outlier: 3.533A pdb=" N VAL A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 155 through 189 removed outlier: 3.558A pdb=" N PHE A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 179 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 209 removed outlier: 3.983A pdb=" N PHE A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.591A pdb=" N VAL A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 240 removed outlier: 3.585A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.629A pdb=" N VAL A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.534A pdb=" N SER A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 312 removed outlier: 3.558A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 321 removed outlier: 3.800A pdb=" N TRP A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.567A pdb=" N HIS A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.948A pdb=" N LEU A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 removed outlier: 3.771A pdb=" N PHE A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.795A pdb=" N ALA A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 414 removed outlier: 3.575A pdb=" N ALA A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N SER A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 454 removed outlier: 4.077A pdb=" N LYS A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE A 431 " --> pdb=" O GLN A 427 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.618A pdb=" N LEU A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 480 removed outlier: 3.725A pdb=" N ILE A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 512 removed outlier: 3.522A pdb=" N ALA A 489 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 508 " --> pdb=" O TRP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.733A pdb=" N GLY A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 548 removed outlier: 3.750A pdb=" N GLY A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS A 541 " --> pdb=" O GLY A 537 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 542 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 548 " --> pdb=" O CYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 560 removed outlier: 3.770A pdb=" N ILE A 560 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 605 removed outlier: 3.786A pdb=" N VAL A 598 " --> pdb=" O LYS A 594 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 599 " --> pdb=" O TRP A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.503A pdb=" N LEU A 612 " --> pdb=" O PRO A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 620 through 643 removed outlier: 3.721A pdb=" N PHE A 624 " --> pdb=" O GLY A 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.620A pdb=" N TYR B 13 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 61 removed outlier: 3.595A pdb=" N GLY B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 removed outlier: 3.507A pdb=" N GLN B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 removed outlier: 4.482A pdb=" N SER B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 4.327A pdb=" N PHE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 137 removed outlier: 3.533A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 155 through 189 removed outlier: 3.558A pdb=" N PHE B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 168 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 179 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 209 removed outlier: 3.983A pdb=" N PHE B 197 " --> pdb=" O TYR B 193 " (cutoff:3.500A) Proline residue: B 200 - end of helix removed outlier: 3.591A pdb=" N VAL B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 240 removed outlier: 3.585A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR B 238 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.630A pdb=" N VAL B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 255 " --> pdb=" O TYR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 285 removed outlier: 3.534A pdb=" N SER B 285 " --> pdb=" O PHE B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 312 removed outlier: 3.559A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.801A pdb=" N TRP B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 removed outlier: 3.567A pdb=" N HIS B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.948A pdb=" N LEU B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 356 removed outlier: 3.771A pdb=" N PHE B 343 " --> pdb=" O PHE B 339 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 346 " --> pdb=" O PRO B 342 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 351 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.795A pdb=" N ALA B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 414 removed outlier: 3.575A pdb=" N ALA B 394 " --> pdb=" O MET B 390 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N SER B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 454 removed outlier: 4.073A pdb=" N LYS B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 463 through 469 removed outlier: 3.617A pdb=" N LEU B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 480 removed outlier: 3.726A pdb=" N ILE B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 512 removed outlier: 3.522A pdb=" N ALA B 489 " --> pdb=" O ASN B 485 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 508 " --> pdb=" O TRP B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.733A pdb=" N GLY B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 548 removed outlier: 3.750A pdb=" N GLY B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS B 541 " --> pdb=" O GLY B 537 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 542 " --> pdb=" O GLY B 538 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 548 " --> pdb=" O CYS B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 560 removed outlier: 3.770A pdb=" N ILE B 560 " --> pdb=" O THR B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 605 removed outlier: 3.786A pdb=" N VAL B 598 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 599 " --> pdb=" O TRP B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 removed outlier: 3.503A pdb=" N LEU B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 620 through 643 removed outlier: 3.721A pdb=" N PHE B 624 " --> pdb=" O GLY B 620 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1375 1.32 - 1.44: 2645 1.44 - 1.57: 5371 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 9455 Sorted by residual: bond pdb=" N ILE B 419 " pdb=" CA ILE B 419 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.23e-02 6.61e+03 1.17e+01 bond pdb=" N ILE A 419 " pdb=" CA ILE A 419 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.32e-02 5.74e+03 9.57e+00 bond pdb=" N ILE A 89 " pdb=" CA ILE A 89 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" N ILE B 89 " pdb=" CA ILE B 89 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" N ILE A 404 " pdb=" CA ILE A 404 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.35e+00 ... (remaining 9450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 12380 1.56 - 3.13: 375 3.13 - 4.69: 115 4.69 - 6.26: 16 6.26 - 7.82: 8 Bond angle restraints: 12894 Sorted by residual: angle pdb=" N ALA A 405 " pdb=" CA ALA A 405 " pdb=" C ALA A 405 " ideal model delta sigma weight residual 114.31 106.49 7.82 1.29e+00 6.01e-01 3.67e+01 angle pdb=" N ALA B 405 " pdb=" CA ALA B 405 " pdb=" C ALA B 405 " ideal model delta sigma weight residual 114.31 106.50 7.81 1.29e+00 6.01e-01 3.67e+01 angle pdb=" CA PHE A 49 " pdb=" CB PHE A 49 " pdb=" CG PHE A 49 " ideal model delta sigma weight residual 113.80 109.94 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA PHE B 49 " pdb=" CB PHE B 49 " pdb=" CG PHE B 49 " ideal model delta sigma weight residual 113.80 109.94 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA ARG B 137 " pdb=" C ARG B 137 " pdb=" N LYS B 138 " ideal model delta sigma weight residual 118.13 123.04 -4.91 1.28e+00 6.10e-01 1.47e+01 ... (remaining 12889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4877 17.65 - 35.30: 505 35.30 - 52.95: 161 52.95 - 70.60: 26 70.60 - 88.25: 10 Dihedral angle restraints: 5579 sinusoidal: 2209 harmonic: 3370 Sorted by residual: dihedral pdb=" CD ARG B 586 " pdb=" NE ARG B 586 " pdb=" CZ ARG B 586 " pdb=" NH1 ARG B 586 " ideal model delta sinusoidal sigma weight residual 0.00 -74.74 74.74 1 1.00e+01 1.00e-02 7.07e+01 dihedral pdb=" CD ARG A 586 " pdb=" NE ARG A 586 " pdb=" CZ ARG A 586 " pdb=" NH1 ARG A 586 " ideal model delta sinusoidal sigma weight residual 0.00 -74.54 74.54 1 1.00e+01 1.00e-02 7.04e+01 dihedral pdb=" CD ARG A 137 " pdb=" NE ARG A 137 " pdb=" CZ ARG A 137 " pdb=" NH1 ARG A 137 " ideal model delta sinusoidal sigma weight residual 0.00 -39.94 39.94 1 1.00e+01 1.00e-02 2.24e+01 ... (remaining 5576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1044 0.039 - 0.078: 391 0.078 - 0.118: 80 0.118 - 0.157: 16 0.157 - 0.196: 7 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA ARG B 514 " pdb=" N ARG B 514 " pdb=" C ARG B 514 " pdb=" CB ARG B 514 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA ARG A 514 " pdb=" N ARG A 514 " pdb=" C ARG A 514 " pdb=" CB ARG A 514 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA PHE A 49 " pdb=" N PHE A 49 " pdb=" C PHE A 49 " pdb=" CB PHE A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 1535 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 586 " -1.042 9.50e-02 1.11e+02 4.67e-01 1.32e+02 pdb=" NE ARG A 586 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 586 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 586 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 586 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 586 " 1.042 9.50e-02 1.11e+02 4.67e-01 1.32e+02 pdb=" NE ARG B 586 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 586 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 586 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 586 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 137 " 0.697 9.50e-02 1.11e+02 3.13e-01 5.95e+01 pdb=" NE ARG A 137 " -0.041 2.00e-02 2.50e+03 pdb=" CZ ARG A 137 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 137 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 137 " 0.022 2.00e-02 2.50e+03 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1573 2.76 - 3.30: 8347 3.30 - 3.83: 14675 3.83 - 4.37: 17314 4.37 - 4.90: 31345 Nonbonded interactions: 73254 Sorted by model distance: nonbonded pdb=" OG SER B 25 " pdb=" OE1 GLU B 364 " model vdw 2.228 3.040 nonbonded pdb=" OG SER A 25 " pdb=" OE1 GLU A 364 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 552 " pdb=" OG1 THR A 556 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR B 552 " pdb=" OG1 THR B 556 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASN A 281 " pdb=" OG SER A 291 " model vdw 2.296 3.040 ... (remaining 73249 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 801 or resid 803)) selection = (chain 'B' and (resid 5 through 801 or resid 803)) } 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: 5.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.880 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 0.042 9457 Z= 0.243 Angle : 0.686 7.820 12898 Z= 0.421 Chirality : 0.043 0.196 1538 Planarity : 0.024 0.467 1528 Dihedral : 16.165 88.251 3429 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 0.21 % Allowed : 21.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.25), residues: 1178 helix: 0.52 (0.19), residues: 842 sheet: None (None), residues: 0 loop : -2.36 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 586 TYR 0.014 0.001 TYR B 418 PHE 0.030 0.001 PHE A 49 TRP 0.012 0.001 TRP A 504 HIS 0.003 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9455) covalent geometry : angle 0.68621 (12894) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.50973 ( 4) hydrogen bonds : bond 0.22439 ( 568) hydrogen bonds : angle 7.54497 ( 1686) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.359 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.7098 time to fit residues: 79.6927 Evaluate side-chains 89 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 117 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 511 GLN B 313 ASN B 420 ASN B 511 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107037 restraints weight = 10902.439| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.58 r_work: 0.3070 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9457 Z= 0.182 Angle : 0.636 6.953 12898 Z= 0.323 Chirality : 0.043 0.141 1538 Planarity : 0.006 0.069 1528 Dihedral : 9.058 58.305 1587 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.16 % Allowed : 21.73 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.25), residues: 1178 helix: 0.74 (0.19), residues: 858 sheet: None (None), residues: 0 loop : -2.10 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 426 TYR 0.010 0.001 TYR B 512 PHE 0.023 0.002 PHE B 49 TRP 0.014 0.001 TRP B 625 HIS 0.004 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9455) covalent geometry : angle 0.63577 (12894) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.62374 ( 4) hydrogen bonds : bond 0.07029 ( 568) hydrogen bonds : angle 4.83203 ( 1686) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.347 Fit side-chains REVERT: A 123 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7452 (mt) REVERT: A 243 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: B 123 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7468 (mt) REVERT: B 243 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7422 (mt-10) outliers start: 30 outliers final: 20 residues processed: 112 average time/residue: 0.5717 time to fit residues: 68.8240 Evaluate side-chains 108 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 53 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN A 511 GLN B 420 ASN B 511 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.109574 restraints weight = 10829.353| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.59 r_work: 0.3103 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9457 Z= 0.131 Angle : 0.557 6.412 12898 Z= 0.282 Chirality : 0.040 0.126 1538 Planarity : 0.005 0.059 1528 Dihedral : 8.761 59.115 1587 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.16 % Allowed : 21.41 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.25), residues: 1178 helix: 0.88 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -2.09 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 514 TYR 0.007 0.001 TYR B 512 PHE 0.015 0.001 PHE B 49 TRP 0.013 0.001 TRP A 504 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9455) covalent geometry : angle 0.55695 (12894) SS BOND : bond 0.00318 ( 2) SS BOND : angle 0.62169 ( 4) hydrogen bonds : bond 0.05541 ( 568) hydrogen bonds : angle 4.49386 ( 1686) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.326 Fit side-chains REVERT: A 382 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7798 (m) REVERT: A 441 CYS cc_start: 0.8372 (t) cc_final: 0.7922 (m) REVERT: A 581 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.5987 (ttm-80) REVERT: B 243 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: B 382 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7801 (m) REVERT: B 441 CYS cc_start: 0.8373 (t) cc_final: 0.7922 (m) REVERT: B 581 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.5991 (ttm-80) outliers start: 30 outliers final: 18 residues processed: 110 average time/residue: 0.5131 time to fit residues: 61.0963 Evaluate side-chains 112 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 581 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.137713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108649 restraints weight = 10888.552| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.58 r_work: 0.3097 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9457 Z= 0.160 Angle : 0.592 6.815 12898 Z= 0.299 Chirality : 0.042 0.124 1538 Planarity : 0.005 0.055 1528 Dihedral : 8.786 58.924 1587 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.90 % Allowed : 20.68 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1178 helix: 0.89 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -2.06 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 514 TYR 0.008 0.001 TYR B 512 PHE 0.017 0.002 PHE A 49 TRP 0.013 0.001 TRP B 504 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9455) covalent geometry : angle 0.59245 (12894) SS BOND : bond 0.00365 ( 2) SS BOND : angle 0.69985 ( 4) hydrogen bonds : bond 0.06096 ( 568) hydrogen bonds : angle 4.44457 ( 1686) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.277 Fit side-chains REVERT: A 382 SER cc_start: 0.8076 (OUTLIER) cc_final: 0.7719 (m) REVERT: A 441 CYS cc_start: 0.8331 (t) cc_final: 0.7850 (m) REVERT: A 581 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.5910 (ttm-80) REVERT: B 382 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7724 (m) REVERT: B 441 CYS cc_start: 0.8328 (t) cc_final: 0.7847 (m) REVERT: B 581 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.5947 (ttm-80) outliers start: 37 outliers final: 28 residues processed: 120 average time/residue: 0.5092 time to fit residues: 66.1960 Evaluate side-chains 121 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.137643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.108548 restraints weight = 10791.877| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.57 r_work: 0.3079 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9457 Z= 0.158 Angle : 0.592 6.749 12898 Z= 0.299 Chirality : 0.042 0.124 1538 Planarity : 0.005 0.055 1528 Dihedral : 8.769 59.260 1587 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.64 % Allowed : 20.68 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.25), residues: 1178 helix: 0.90 (0.18), residues: 858 sheet: None (None), residues: 0 loop : -2.04 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 581 TYR 0.008 0.001 TYR A 512 PHE 0.017 0.002 PHE B 49 TRP 0.013 0.001 TRP B 625 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9455) covalent geometry : angle 0.59167 (12894) SS BOND : bond 0.00375 ( 2) SS BOND : angle 0.73510 ( 4) hydrogen bonds : bond 0.06017 ( 568) hydrogen bonds : angle 4.42372 ( 1686) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 95 time to evaluate : 0.390 Fit side-chains REVERT: A 123 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7460 (mt) REVERT: A 382 SER cc_start: 0.8156 (OUTLIER) cc_final: 0.7812 (m) REVERT: A 441 CYS cc_start: 0.8367 (t) cc_final: 0.7910 (m) REVERT: A 581 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.5937 (ttm-80) REVERT: B 123 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7480 (mt) REVERT: B 382 SER cc_start: 0.8156 (OUTLIER) cc_final: 0.7818 (m) REVERT: B 441 CYS cc_start: 0.8369 (t) cc_final: 0.7910 (m) REVERT: B 581 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.5961 (ttm-80) outliers start: 44 outliers final: 34 residues processed: 127 average time/residue: 0.4667 time to fit residues: 64.4719 Evaluate side-chains 129 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 0.0670 chunk 29 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.139455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110361 restraints weight = 10858.154| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.58 r_work: 0.2981 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9457 Z= 0.130 Angle : 0.552 6.487 12898 Z= 0.279 Chirality : 0.040 0.121 1538 Planarity : 0.005 0.053 1528 Dihedral : 8.616 59.959 1587 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.69 % Allowed : 21.94 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.25), residues: 1178 helix: 1.04 (0.18), residues: 858 sheet: None (None), residues: 0 loop : -1.97 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 581 TYR 0.007 0.001 TYR A 512 PHE 0.016 0.001 PHE B 49 TRP 0.013 0.001 TRP B 625 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9455) covalent geometry : angle 0.55235 (12894) SS BOND : bond 0.00293 ( 2) SS BOND : angle 0.63851 ( 4) hydrogen bonds : bond 0.05273 ( 568) hydrogen bonds : angle 4.33619 ( 1686) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.353 Fit side-chains REVERT: A 49 PHE cc_start: 0.6340 (OUTLIER) cc_final: 0.5479 (t80) REVERT: A 382 SER cc_start: 0.8029 (OUTLIER) cc_final: 0.7696 (m) REVERT: A 441 CYS cc_start: 0.8242 (t) cc_final: 0.7788 (m) REVERT: A 581 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.5769 (ttm-80) REVERT: B 49 PHE cc_start: 0.6354 (OUTLIER) cc_final: 0.5493 (t80) REVERT: B 382 SER cc_start: 0.8019 (OUTLIER) cc_final: 0.7691 (m) REVERT: B 441 CYS cc_start: 0.8243 (t) cc_final: 0.7788 (m) REVERT: B 581 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.5815 (ttm-80) outliers start: 35 outliers final: 27 residues processed: 113 average time/residue: 0.5280 time to fit residues: 64.5425 Evaluate side-chains 125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 0.0770 chunk 110 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.140029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110893 restraints weight = 10819.436| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.58 r_work: 0.3086 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9457 Z= 0.125 Angle : 0.544 6.489 12898 Z= 0.274 Chirality : 0.040 0.121 1538 Planarity : 0.005 0.053 1528 Dihedral : 8.534 59.618 1587 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.32 % Allowed : 21.31 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.25), residues: 1178 helix: 1.13 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -1.97 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 581 TYR 0.007 0.001 TYR A 512 PHE 0.016 0.001 PHE A 49 TRP 0.012 0.001 TRP B 625 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9455) covalent geometry : angle 0.54349 (12894) SS BOND : bond 0.00278 ( 2) SS BOND : angle 0.61730 ( 4) hydrogen bonds : bond 0.05112 ( 568) hydrogen bonds : angle 4.29452 ( 1686) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 0.342 Fit side-chains REVERT: A 49 PHE cc_start: 0.6441 (OUTLIER) cc_final: 0.5608 (t80) REVERT: A 382 SER cc_start: 0.8098 (OUTLIER) cc_final: 0.7771 (m) REVERT: A 441 CYS cc_start: 0.8285 (t) cc_final: 0.7844 (m) REVERT: A 581 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.5815 (ttm-80) REVERT: B 49 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.5583 (t80) REVERT: B 382 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7771 (m) REVERT: B 441 CYS cc_start: 0.8273 (t) cc_final: 0.7832 (m) REVERT: B 581 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5848 (ttm-80) outliers start: 41 outliers final: 29 residues processed: 121 average time/residue: 0.4804 time to fit residues: 63.0997 Evaluate side-chains 123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 69 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.141677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.112760 restraints weight = 10702.825| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.55 r_work: 0.3122 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9457 Z= 0.110 Angle : 0.520 6.470 12898 Z= 0.262 Chirality : 0.039 0.119 1538 Planarity : 0.005 0.052 1528 Dihedral : 8.398 59.799 1587 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.74 % Allowed : 22.78 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.25), residues: 1178 helix: 1.28 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -1.96 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 581 TYR 0.007 0.001 TYR A 512 PHE 0.015 0.001 PHE B 49 TRP 0.012 0.001 TRP A 625 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9455) covalent geometry : angle 0.51958 (12894) SS BOND : bond 0.00233 ( 2) SS BOND : angle 0.53234 ( 4) hydrogen bonds : bond 0.04594 ( 568) hydrogen bonds : angle 4.22863 ( 1686) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.356 Fit side-chains REVERT: A 49 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.5627 (t80) REVERT: B 49 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.5641 (t80) REVERT: B 581 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.5773 (ttm-80) outliers start: 26 outliers final: 18 residues processed: 110 average time/residue: 0.5301 time to fit residues: 62.9013 Evaluate side-chains 113 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 91 optimal weight: 0.0770 chunk 63 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.142179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113409 restraints weight = 10661.233| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.55 r_work: 0.3007 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9457 Z= 0.115 Angle : 0.531 7.198 12898 Z= 0.266 Chirality : 0.039 0.120 1538 Planarity : 0.005 0.052 1528 Dihedral : 8.368 59.108 1587 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.38 % Allowed : 22.57 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.25), residues: 1178 helix: 1.34 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -1.93 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 514 TYR 0.006 0.001 TYR A 512 PHE 0.016 0.001 PHE A 49 TRP 0.012 0.001 TRP B 504 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9455) covalent geometry : angle 0.53061 (12894) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.55936 ( 4) hydrogen bonds : bond 0.04746 ( 568) hydrogen bonds : angle 4.22543 ( 1686) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.310 Fit side-chains REVERT: A 49 PHE cc_start: 0.6376 (OUTLIER) cc_final: 0.5535 (t80) REVERT: A 382 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7691 (m) REVERT: B 49 PHE cc_start: 0.6384 (OUTLIER) cc_final: 0.5538 (t80) REVERT: B 382 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7687 (m) REVERT: B 581 ARG cc_start: 0.6402 (OUTLIER) cc_final: 0.5694 (ttm-80) outliers start: 32 outliers final: 25 residues processed: 112 average time/residue: 0.5069 time to fit residues: 61.5606 Evaluate side-chains 121 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 1.9990 chunk 112 optimal weight: 0.0670 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.140504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111601 restraints weight = 10763.098| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.54 r_work: 0.3103 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9457 Z= 0.123 Angle : 0.542 7.405 12898 Z= 0.272 Chirality : 0.040 0.121 1538 Planarity : 0.005 0.052 1528 Dihedral : 8.364 57.947 1587 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.48 % Allowed : 22.68 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.25), residues: 1178 helix: 1.34 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -1.94 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 514 TYR 0.007 0.001 TYR A 512 PHE 0.016 0.001 PHE B 49 TRP 0.012 0.001 TRP B 504 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9455) covalent geometry : angle 0.54174 (12894) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.62159 ( 4) hydrogen bonds : bond 0.04996 ( 568) hydrogen bonds : angle 4.24660 ( 1686) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.354 Fit side-chains REVERT: A 49 PHE cc_start: 0.6441 (OUTLIER) cc_final: 0.5582 (t80) REVERT: A 382 SER cc_start: 0.8090 (OUTLIER) cc_final: 0.7779 (m) REVERT: B 49 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.5586 (t80) REVERT: B 382 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7783 (m) REVERT: B 581 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.5730 (ttm-80) outliers start: 33 outliers final: 24 residues processed: 110 average time/residue: 0.5130 time to fit residues: 61.1382 Evaluate side-chains 119 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 581 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.134545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106655 restraints weight = 10711.164| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.38 r_work: 0.3049 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9457 Z= 0.234 Angle : 0.690 8.954 12898 Z= 0.346 Chirality : 0.046 0.132 1538 Planarity : 0.005 0.053 1528 Dihedral : 8.955 58.540 1587 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.95 % Allowed : 22.78 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.25), residues: 1178 helix: 0.94 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -2.03 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.013 0.002 TYR A 512 PHE 0.021 0.002 PHE B 297 TRP 0.012 0.002 TRP B 504 HIS 0.006 0.002 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 9455) covalent geometry : angle 0.68964 (12894) SS BOND : bond 0.00508 ( 2) SS BOND : angle 0.91684 ( 4) hydrogen bonds : bond 0.07367 ( 568) hydrogen bonds : angle 4.53479 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3198.10 seconds wall clock time: 55 minutes 18.03 seconds (3318.03 seconds total)