Starting phenix.real_space_refine on Mon May 12 18:42:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7d_61202/05_2025/9j7d_61202_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7d_61202/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9j7d_61202/05_2025/9j7d_61202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7d_61202/05_2025/9j7d_61202.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7d_61202/05_2025/9j7d_61202_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7d_61202/05_2025/9j7d_61202_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.57, per 1000 atoms: 0.71 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: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.89 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: 2.38 Time building geometry restraints manager: 2.81 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 646 or resid 801 or resid 803)) selection = (chain 'B' and (resid 5 through 646 or resid 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: 5.370 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.920 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.480 ------------------------------------------------------------------------------- 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 : 4.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.001 TRP A 504 HIS 0.003 0.001 HIS B 222 PHE 0.030 0.001 PHE A 49 TYR 0.014 0.001 TYR B 418 ARG 0.006 0.001 ARG B 586 Details of bonding type rmsd hydrogen bonds : bond 0.22439 ( 568) hydrogen bonds : angle 7.54497 ( 1686) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.50973 ( 4) covalent geometry : bond 0.00367 ( 9455) covalent geometry : angle 0.68621 (12894) *********************** 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 : 1.004 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 1.4189 time to fit residues: 160.1412 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 : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.138165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109163 restraints weight = 10662.703| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.59 r_work: 0.3086 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9457 Z= 0.162 Angle : 0.610 6.654 12898 Z= 0.310 Chirality : 0.042 0.140 1538 Planarity : 0.006 0.067 1528 Dihedral : 8.985 58.377 1587 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.06 % Allowed : 21.73 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1178 helix: 0.76 (0.19), residues: 854 sheet: None (None), residues: 0 loop : -2.10 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 625 HIS 0.003 0.001 HIS B 222 PHE 0.022 0.002 PHE B 49 TYR 0.008 0.001 TYR B 512 ARG 0.005 0.001 ARG B 514 Details of bonding type rmsd hydrogen bonds : bond 0.06683 ( 568) hydrogen bonds : angle 4.80317 ( 1686) SS BOND : bond 0.00376 ( 2) SS BOND : angle 0.54131 ( 4) covalent geometry : bond 0.00377 ( 9455) covalent geometry : angle 0.61005 (12894) *********************** 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 118 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.989 Fit side-chains REVERT: A 243 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: B 243 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7421 (mt-10) outliers start: 29 outliers final: 18 residues processed: 109 average time/residue: 1.1512 time to fit residues: 135.2878 Evaluate side-chains 115 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 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 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 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 74 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.139252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109990 restraints weight = 10921.208| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.59 r_work: 0.3108 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1210 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= 0.126 Angle : 0.549 6.418 12898 Z= 0.278 Chirality : 0.040 0.127 1538 Planarity : 0.005 0.058 1528 Dihedral : 8.735 58.919 1587 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.95 % Allowed : 22.26 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1178 helix: 0.90 (0.18), residues: 858 sheet: None (None), residues: 0 loop : -2.13 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 504 HIS 0.003 0.001 HIS A 222 PHE 0.015 0.001 PHE A 49 TYR 0.007 0.001 TYR B 512 ARG 0.003 0.000 ARG B 514 Details of bonding type rmsd hydrogen bonds : bond 0.05450 ( 568) hydrogen bonds : angle 4.48506 ( 1686) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.59284 ( 4) covalent geometry : bond 0.00281 ( 9455) covalent geometry : angle 0.54865 (12894) *********************** 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 123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.951 Fit side-chains REVERT: A 243 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7358 (mt-10) REVERT: A 441 CYS cc_start: 0.8372 (t) cc_final: 0.7916 (m) REVERT: A 581 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.5980 (ttm-80) REVERT: B 243 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: B 441 CYS cc_start: 0.8367 (t) cc_final: 0.7910 (m) REVERT: B 581 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5988 (ttm-80) outliers start: 28 outliers final: 18 residues processed: 116 average time/residue: 0.9947 time to fit residues: 125.7466 Evaluate side-chains 105 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 243 GLU Chi-restraints excluded: chain A residue 265 THR 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 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 40 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 60 optimal weight: 0.0050 chunk 85 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.140486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111360 restraints weight = 10775.850| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.56 r_work: 0.3142 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9457 Z= 0.109 Angle : 0.518 6.427 12898 Z= 0.261 Chirality : 0.039 0.119 1538 Planarity : 0.005 0.052 1528 Dihedral : 8.489 59.395 1587 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.27 % Allowed : 21.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1178 helix: 1.13 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 504 HIS 0.002 0.001 HIS A 222 PHE 0.015 0.001 PHE B 49 TYR 0.006 0.001 TYR A 512 ARG 0.003 0.000 ARG B 514 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 568) hydrogen bonds : angle 4.28170 ( 1686) SS BOND : bond 0.00227 ( 2) SS BOND : angle 0.46987 ( 4) covalent geometry : bond 0.00235 ( 9455) covalent geometry : angle 0.51813 (12894) *********************** 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 126 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.897 Fit side-chains REVERT: A 49 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.5594 (t80) REVERT: A 441 CYS cc_start: 0.8249 (t) cc_final: 0.7824 (m) REVERT: A 581 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.5910 (ttm-80) REVERT: B 49 PHE cc_start: 0.6455 (OUTLIER) cc_final: 0.5592 (t80) REVERT: B 243 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: B 441 CYS cc_start: 0.8252 (t) cc_final: 0.7823 (m) REVERT: B 581 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.5920 (ttm-80) outliers start: 31 outliers final: 18 residues processed: 112 average time/residue: 0.9974 time to fit residues: 121.2947 Evaluate side-chains 115 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 545 SER Chi-restraints excluded: chain A residue 581 ARG 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 243 GLU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 393 MET 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 51 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.137941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.108708 restraints weight = 10812.861| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.55 r_work: 0.3080 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1450 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= 0.134 Angle : 0.554 6.729 12898 Z= 0.279 Chirality : 0.040 0.122 1538 Planarity : 0.005 0.051 1528 Dihedral : 8.549 59.992 1587 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.69 % Allowed : 21.73 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1178 helix: 1.11 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -1.99 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 504 HIS 0.003 0.001 HIS A 222 PHE 0.016 0.001 PHE B 49 TYR 0.007 0.001 TYR A 512 ARG 0.002 0.000 ARG A 426 Details of bonding type rmsd hydrogen bonds : bond 0.05347 ( 568) hydrogen bonds : angle 4.31888 ( 1686) SS BOND : bond 0.00311 ( 2) SS BOND : angle 0.61699 ( 4) covalent geometry : bond 0.00310 ( 9455) covalent geometry : angle 0.55439 (12894) *********************** 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 127 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.946 Fit side-chains REVERT: A 49 PHE cc_start: 0.6444 (OUTLIER) cc_final: 0.5572 (t80) REVERT: A 581 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.5836 (ttm-80) REVERT: B 49 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.5580 (t80) REVERT: B 581 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.5845 (ttm-80) outliers start: 35 outliers final: 27 residues processed: 115 average time/residue: 0.9321 time to fit residues: 116.9551 Evaluate side-chains 121 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 246 SER Chi-restraints excluded: chain A residue 265 THR 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 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 246 SER Chi-restraints excluded: chain B residue 265 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.136697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107705 restraints weight = 10844.895| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.55 r_work: 0.3086 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9457 Z= 0.178 Angle : 0.618 7.407 12898 Z= 0.311 Chirality : 0.043 0.127 1538 Planarity : 0.005 0.054 1528 Dihedral : 8.770 59.517 1587 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.90 % Allowed : 22.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1178 helix: 1.01 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -2.03 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 504 HIS 0.004 0.001 HIS A 222 PHE 0.018 0.002 PHE A 49 TYR 0.009 0.001 TYR A 512 ARG 0.002 0.000 ARG A 137 Details of bonding type rmsd hydrogen bonds : bond 0.06403 ( 568) hydrogen bonds : angle 4.44100 ( 1686) SS BOND : bond 0.00414 ( 2) SS BOND : angle 0.80859 ( 4) covalent geometry : bond 0.00435 ( 9455) covalent geometry : angle 0.61783 (12894) *********************** 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 127 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.938 Fit side-chains REVERT: A 382 SER cc_start: 0.8126 (OUTLIER) cc_final: 0.7755 (m) REVERT: A 581 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.5851 (ttm-80) REVERT: B 382 SER cc_start: 0.8119 (OUTLIER) cc_final: 0.7753 (m) REVERT: B 581 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.5853 (ttm-80) outliers start: 37 outliers final: 27 residues processed: 116 average time/residue: 1.0393 time to fit residues: 130.9588 Evaluate side-chains 119 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 582 GLU 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 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 556 THR Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 582 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 80 optimal weight: 0.0370 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 0.0980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.141716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.112930 restraints weight = 10846.861| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.55 r_work: 0.3016 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9457 Z= 0.107 Angle : 0.518 6.777 12898 Z= 0.261 Chirality : 0.039 0.120 1538 Planarity : 0.005 0.051 1528 Dihedral : 8.413 59.644 1587 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.85 % Allowed : 23.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1178 helix: 1.22 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -1.96 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 625 HIS 0.002 0.001 HIS A 222 PHE 0.014 0.001 PHE A 49 TYR 0.006 0.001 TYR A 512 ARG 0.002 0.000 ARG B 514 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 568) hydrogen bonds : angle 4.26084 ( 1686) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.50521 ( 4) covalent geometry : bond 0.00226 ( 9455) covalent geometry : angle 0.51818 (12894) *********************** 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 121 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.990 Fit side-chains REVERT: A 382 SER cc_start: 0.7957 (OUTLIER) cc_final: 0.7645 (m) REVERT: A 581 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.5775 (ttm-80) REVERT: B 382 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7645 (m) REVERT: B 581 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.5773 (ttm-80) outliers start: 27 outliers final: 15 residues processed: 110 average time/residue: 1.0188 time to fit residues: 121.7520 Evaluate side-chains 109 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 111 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain B residue 33 LEU 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 265 THR Chi-restraints excluded: chain B residue 382 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 90 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 113 optimal weight: 0.0870 chunk 44 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 = 0.141465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112528 restraints weight = 10902.566| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.56 r_work: 0.3116 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9457 Z= 0.112 Angle : 0.525 7.096 12898 Z= 0.263 Chirality : 0.039 0.122 1538 Planarity : 0.005 0.051 1528 Dihedral : 8.331 59.175 1587 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.74 % Allowed : 23.10 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1178 helix: 1.35 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 625 HIS 0.003 0.001 HIS A 222 PHE 0.016 0.001 PHE A 49 TYR 0.007 0.001 TYR A 512 ARG 0.002 0.000 ARG B 426 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 568) hydrogen bonds : angle 4.23515 ( 1686) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.52861 ( 4) covalent geometry : bond 0.00247 ( 9455) covalent geometry : angle 0.52519 (12894) *********************** 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 115 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.917 Fit side-chains REVERT: A 382 SER cc_start: 0.8009 (OUTLIER) cc_final: 0.7702 (m) REVERT: A 581 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.5819 (ttm-80) REVERT: B 382 SER cc_start: 0.8007 (OUTLIER) cc_final: 0.7699 (m) REVERT: B 581 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.5824 (ttm-80) outliers start: 26 outliers final: 18 residues processed: 105 average time/residue: 1.0625 time to fit residues: 120.6795 Evaluate side-chains 111 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 111 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 126 LEU 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 581 ARG Chi-restraints excluded: chain B residue 33 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.137399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108284 restraints weight = 10753.840| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.56 r_work: 0.3048 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1530 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= 0.174 Angle : 0.609 7.753 12898 Z= 0.306 Chirality : 0.042 0.126 1538 Planarity : 0.005 0.052 1528 Dihedral : 8.617 58.698 1587 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.38 % Allowed : 22.47 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1178 helix: 1.14 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -1.93 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 504 HIS 0.004 0.001 HIS A 222 PHE 0.018 0.002 PHE A 49 TYR 0.010 0.001 TYR A 512 ARG 0.002 0.000 ARG A 137 Details of bonding type rmsd hydrogen bonds : bond 0.06230 ( 568) hydrogen bonds : angle 4.39889 ( 1686) SS BOND : bond 0.00401 ( 2) SS BOND : angle 0.75834 ( 4) covalent geometry : bond 0.00426 ( 9455) covalent geometry : angle 0.60903 (12894) *********************** 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 119 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.978 Fit side-chains REVERT: A 382 SER cc_start: 0.8205 (OUTLIER) cc_final: 0.7853 (m) REVERT: A 581 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.5853 (ttm-80) REVERT: B 382 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7852 (m) REVERT: B 581 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.5849 (ttm-80) outliers start: 32 outliers final: 27 residues processed: 111 average time/residue: 0.9685 time to fit residues: 117.0606 Evaluate side-chains 119 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 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 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 23 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.141878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113190 restraints weight = 10815.343| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.55 r_work: 0.3101 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9457 Z= 0.115 Angle : 0.537 7.486 12898 Z= 0.269 Chirality : 0.039 0.126 1538 Planarity : 0.005 0.051 1528 Dihedral : 8.370 57.940 1587 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.53 % Allowed : 23.31 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1178 helix: 1.29 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -1.93 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 625 HIS 0.003 0.001 HIS B 222 PHE 0.016 0.001 PHE A 49 TYR 0.007 0.001 TYR B 512 ARG 0.001 0.000 ARG A 426 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 568) hydrogen bonds : angle 4.27489 ( 1686) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.57829 ( 4) covalent geometry : bond 0.00254 ( 9455) covalent geometry : angle 0.53652 (12894) ********************** 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 109 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.867 Fit side-chains REVERT: A 382 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7753 (m) REVERT: A 581 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5835 (ttm-80) REVERT: B 382 SER cc_start: 0.8079 (OUTLIER) cc_final: 0.7749 (m) REVERT: B 581 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.5841 (ttm-80) outliers start: 24 outliers final: 19 residues processed: 101 average time/residue: 1.0405 time to fit residues: 113.7652 Evaluate side-chains 108 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU 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 265 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 556 THR 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 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 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 48 optimal weight: 0.0370 chunk 26 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.0570 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.145078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116326 restraints weight = 10678.659| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.55 r_work: 0.3182 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9457 Z= 0.096 Angle : 0.497 7.360 12898 Z= 0.248 Chirality : 0.038 0.119 1538 Planarity : 0.004 0.051 1528 Dihedral : 8.035 57.161 1587 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.22 % Allowed : 23.63 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1178 helix: 1.57 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -1.89 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 625 HIS 0.002 0.001 HIS B 227 PHE 0.016 0.001 PHE A 49 TYR 0.006 0.001 TYR A 512 ARG 0.001 0.000 ARG B 514 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 568) hydrogen bonds : angle 4.12555 ( 1686) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.42988 ( 4) covalent geometry : bond 0.00201 ( 9455) covalent geometry : angle 0.49727 (12894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5982.17 seconds wall clock time: 103 minutes 52.07 seconds (6232.07 seconds total)