Starting phenix.real_space_refine on Sat Jul 4 18:20:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wj3_37577/07_2026/8wj3_37577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wj3_37577/07_2026/8wj3_37577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wj3_37577/07_2026/8wj3_37577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wj3_37577/07_2026/8wj3_37577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wj3_37577/07_2026/8wj3_37577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wj3_37577/07_2026/8wj3_37577.map" } resolution = 3.36 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 55 5.16 5 C 14379 2.51 5 N 3901 2.21 5 O 4301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22648 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3837 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 478} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "M" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4757 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 29, 'TRANS': 600} Chain breaks: 4 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 7, 'GLU:plan': 11, 'HIS:plan': 4, 'ARG:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 164 Chain: "N" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 3982 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 24, 'TRANS': 517} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 404 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 6, 'TYR:plan': 6, 'PHE:plan': 4, 'TRP:plan': 3, 'GLU:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 206 Chain: "O" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5015 Classifications: {'peptide': 657} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 30, 'TRANS': 626} Chain breaks: 3 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'HIS:plan': 4, 'TYR:plan': 4, 'GLU:plan': 9, 'ASN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 128 Chain: "L" Number of atoms: 4961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 4961 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 30, 'TRANS': 613} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'HIS:plan': 4, 'TYR:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 85 Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.58, per 1000 atoms: 0.25 Number of scatterers: 22648 At special positions: 0 Unit cell: (119.412, 142.003, 147.382, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 9 15.00 Mg 3 11.99 O 4301 8.00 N 3901 7.00 C 14379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5448 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 20 sheets defined 36.4% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.515A pdb=" N VAL D 82 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 131 Processing helix chain 'D' and resid 155 through 161 Processing helix chain 'D' and resid 168 through 171 Processing helix chain 'D' and resid 172 through 185 removed outlier: 3.692A pdb=" N THR D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.652A pdb=" N ALA D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE D 208 " --> pdb=" O TYR D 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 203 through 208' Processing helix chain 'D' and resid 234 through 244 Processing helix chain 'D' and resid 248 through 269 removed outlier: 3.721A pdb=" N ASN D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.974A pdb=" N LEU D 279 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 299 removed outlier: 3.613A pdb=" N ALA D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 372 removed outlier: 3.521A pdb=" N LEU D 364 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS D 372 " --> pdb=" O ALA D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 378 removed outlier: 3.970A pdb=" N PHE D 378 " --> pdb=" O ARG D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 405 removed outlier: 4.245A pdb=" N LEU D 400 " --> pdb=" O ASP D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 422 No H-bonds generated for 'chain 'D' and resid 420 through 422' Processing helix chain 'D' and resid 423 through 441 removed outlier: 3.720A pdb=" N ILE D 428 " --> pdb=" O LEU D 424 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP D 441 " --> pdb=" O ASP D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 464 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 485 through 488 removed outlier: 3.572A pdb=" N GLY D 488 " --> pdb=" O ARG D 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 485 through 488' Processing helix chain 'D' and resid 502 through 509 removed outlier: 3.544A pdb=" N GLN D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 529 removed outlier: 3.745A pdb=" N HIS D 525 " --> pdb=" O SER D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 544 Processing helix chain 'M' and resid 70 through 74 removed outlier: 3.709A pdb=" N GLY M 73 " --> pdb=" O VAL M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 131 Processing helix chain 'M' and resid 155 through 161 Processing helix chain 'M' and resid 173 through 185 removed outlier: 3.913A pdb=" N SER M 179 " --> pdb=" O THR M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 233 Processing helix chain 'M' and resid 234 through 243 removed outlier: 3.540A pdb=" N VAL M 241 " --> pdb=" O GLU M 237 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE M 243 " --> pdb=" O LEU M 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 269 removed outlier: 3.706A pdb=" N ASN M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU M 260 " --> pdb=" O ASP M 256 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU M 266 " --> pdb=" O LYS M 262 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS M 267 " --> pdb=" O LEU M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 299 Processing helix chain 'M' and resid 311 through 315 removed outlier: 3.604A pdb=" N GLU M 315 " --> pdb=" O GLU M 312 " (cutoff:3.500A) Processing helix chain 'M' and resid 360 through 371 removed outlier: 3.545A pdb=" N SER M 369 " --> pdb=" O GLU M 365 " (cutoff:3.500A) Processing helix chain 'M' and resid 372 through 375 removed outlier: 5.959A pdb=" N ARG M 375 " --> pdb=" O LYS M 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 372 through 375' Processing helix chain 'M' and resid 376 through 381 Processing helix chain 'M' and resid 396 through 405 removed outlier: 4.046A pdb=" N LEU M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 422 No H-bonds generated for 'chain 'M' and resid 420 through 422' Processing helix chain 'M' and resid 423 through 439 Processing helix chain 'M' and resid 471 through 484 removed outlier: 4.106A pdb=" N ASP M 475 " --> pdb=" O GLY M 471 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS M 479 " --> pdb=" O ASP M 475 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE M 480 " --> pdb=" O GLY M 476 " (cutoff:3.500A) Processing helix chain 'M' and resid 497 through 501 removed outlier: 3.578A pdb=" N GLU M 500 " --> pdb=" O ARG M 497 " (cutoff:3.500A) Processing helix chain 'M' and resid 502 through 508 Processing helix chain 'M' and resid 519 through 528 removed outlier: 3.639A pdb=" N ARG M 523 " --> pdb=" O ASN M 519 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS M 525 " --> pdb=" O SER M 521 " (cutoff:3.500A) Processing helix chain 'M' and resid 534 through 539 removed outlier: 3.612A pdb=" N GLY M 539 " --> pdb=" O GLU M 535 " (cutoff:3.500A) Processing helix chain 'M' and resid 540 through 544 removed outlier: 3.893A pdb=" N LEU M 544 " --> pdb=" O LEU M 541 " (cutoff:3.500A) Processing helix chain 'M' and resid 579 through 585 removed outlier: 3.813A pdb=" N SER M 585 " --> pdb=" O THR M 581 " (cutoff:3.500A) Processing helix chain 'M' and resid 592 through 603 removed outlier: 4.164A pdb=" N VAL M 596 " --> pdb=" O ASP M 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR M 598 " --> pdb=" O LYS M 594 " (cutoff:3.500A) Processing helix chain 'M' and resid 655 through 657 No H-bonds generated for 'chain 'M' and resid 655 through 657' Processing helix chain 'M' and resid 666 through 677 removed outlier: 3.941A pdb=" N HIS M 670 " --> pdb=" O PRO M 666 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU M 677 " --> pdb=" O LEU M 673 " (cutoff:3.500A) Processing helix chain 'M' and resid 682 through 687 removed outlier: 4.328A pdb=" N GLN M 686 " --> pdb=" O PHE M 682 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 130 removed outlier: 3.595A pdb=" N LEU N 126 " --> pdb=" O THR N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 161 Processing helix chain 'N' and resid 168 through 171 Processing helix chain 'N' and resid 172 through 184 removed outlier: 3.773A pdb=" N THR N 176 " --> pdb=" O GLY N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 233 Processing helix chain 'N' and resid 234 through 243 removed outlier: 3.647A pdb=" N SER N 240 " --> pdb=" O ASP N 236 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL N 241 " --> pdb=" O GLU N 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 248 through 269 removed outlier: 3.922A pdb=" N ASN N 252 " --> pdb=" O GLY N 248 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU N 260 " --> pdb=" O ASP N 256 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU N 261 " --> pdb=" O LYS N 257 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG N 268 " --> pdb=" O GLN N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 288 through 298 Processing helix chain 'N' and resid 360 through 373 removed outlier: 3.701A pdb=" N LEU N 370 " --> pdb=" O GLY N 366 " (cutoff:3.500A) Processing helix chain 'N' and resid 376 through 381 Processing helix chain 'N' and resid 396 through 405 removed outlier: 3.715A pdb=" N LEU N 400 " --> pdb=" O ASP N 396 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU N 401 " --> pdb=" O LEU N 397 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU N 402 " --> pdb=" O ASP N 398 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP N 404 " --> pdb=" O LEU N 400 " (cutoff:3.500A) Processing helix chain 'N' and resid 423 through 441 removed outlier: 3.548A pdb=" N ILE N 428 " --> pdb=" O LEU N 424 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER N 438 " --> pdb=" O ILE N 434 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU N 439 " --> pdb=" O LEU N 435 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 465 removed outlier: 4.060A pdb=" N TYR N 464 " --> pdb=" O GLU N 460 " (cutoff:3.500A) Processing helix chain 'N' and resid 471 through 484 removed outlier: 4.436A pdb=" N ASP N 475 " --> pdb=" O GLY N 471 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE N 480 " --> pdb=" O GLY N 476 " (cutoff:3.500A) Processing helix chain 'N' and resid 497 through 501 Processing helix chain 'N' and resid 502 through 507 Processing helix chain 'N' and resid 519 through 529 removed outlier: 3.594A pdb=" N ASN N 524 " --> pdb=" O SER N 520 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS N 525 " --> pdb=" O SER N 521 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU N 527 " --> pdb=" O ARG N 523 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA N 529 " --> pdb=" O HIS N 525 " (cutoff:3.500A) Processing helix chain 'N' and resid 534 through 540 removed outlier: 3.859A pdb=" N MET N 540 " --> pdb=" O GLY N 536 " (cutoff:3.500A) Processing helix chain 'N' and resid 541 through 544 removed outlier: 3.684A pdb=" N LEU N 544 " --> pdb=" O LEU N 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 541 through 544' Processing helix chain 'N' and resid 579 through 586 removed outlier: 3.823A pdb=" N ASN N 586 " --> pdb=" O ALA N 582 " (cutoff:3.500A) Processing helix chain 'N' and resid 592 through 603 removed outlier: 4.497A pdb=" N VAL N 596 " --> pdb=" O ASP N 592 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR N 598 " --> pdb=" O LYS N 594 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG N 601 " --> pdb=" O LEU N 597 " (cutoff:3.500A) Processing helix chain 'N' and resid 666 through 677 removed outlier: 3.759A pdb=" N HIS N 670 " --> pdb=" O PRO N 666 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU N 672 " --> pdb=" O THR N 668 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU N 677 " --> pdb=" O LEU N 673 " (cutoff:3.500A) Processing helix chain 'N' and resid 680 through 687 removed outlier: 3.748A pdb=" N GLN N 686 " --> pdb=" O PHE N 682 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 75 removed outlier: 4.089A pdb=" N VAL O 75 " --> pdb=" O ALA O 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 72 through 75' Processing helix chain 'O' and resid 76 through 83 Processing helix chain 'O' and resid 122 through 131 Processing helix chain 'O' and resid 155 through 161 Processing helix chain 'O' and resid 168 through 171 Processing helix chain 'O' and resid 172 through 185 removed outlier: 3.612A pdb=" N SER O 185 " --> pdb=" O LEU O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 234 through 243 Processing helix chain 'O' and resid 248 through 268 removed outlier: 3.960A pdb=" N ASN O 252 " --> pdb=" O GLY O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 288 through 302 Processing helix chain 'O' and resid 311 through 315 Processing helix chain 'O' and resid 360 through 373 Processing helix chain 'O' and resid 376 through 381 Processing helix chain 'O' and resid 396 through 405 Processing helix chain 'O' and resid 423 through 441 removed outlier: 3.601A pdb=" N LEU O 427 " --> pdb=" O ILE O 423 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE O 428 " --> pdb=" O LEU O 424 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG O 433 " --> pdb=" O GLY O 429 " (cutoff:3.500A) Processing helix chain 'O' and resid 461 through 464 Processing helix chain 'O' and resid 472 through 488 removed outlier: 5.964A pdb=" N ARG O 485 " --> pdb=" O VAL O 481 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LYS O 486 " --> pdb=" O LYS O 482 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR O 487 " --> pdb=" O GLU O 483 " (cutoff:3.500A) Processing helix chain 'O' and resid 497 through 501 Processing helix chain 'O' and resid 504 through 508 Processing helix chain 'O' and resid 519 through 528 removed outlier: 4.038A pdb=" N ARG O 523 " --> pdb=" O ASN O 519 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN O 524 " --> pdb=" O SER O 520 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS O 525 " --> pdb=" O SER O 521 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU O 527 " --> pdb=" O ARG O 523 " (cutoff:3.500A) Processing helix chain 'O' and resid 536 through 544 removed outlier: 3.590A pdb=" N GLY O 539 " --> pdb=" O GLY O 536 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET O 540 " --> pdb=" O LEU O 537 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU O 541 " --> pdb=" O MET O 538 " (cutoff:3.500A) Proline residue: O 542 - end of helix No H-bonds generated for 'chain 'O' and resid 536 through 544' Processing helix chain 'O' and resid 579 through 586 removed outlier: 3.978A pdb=" N ASN O 586 " --> pdb=" O ALA O 582 " (cutoff:3.500A) Processing helix chain 'O' and resid 592 through 603 removed outlier: 4.436A pdb=" N VAL O 596 " --> pdb=" O ASP O 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 666 through 677 removed outlier: 3.645A pdb=" N HIS O 670 " --> pdb=" O PRO O 666 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU O 672 " --> pdb=" O THR O 668 " (cutoff:3.500A) Processing helix chain 'O' and resid 681 through 687 removed outlier: 3.562A pdb=" N ILE O 687 " --> pdb=" O PHE O 683 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 131 Processing helix chain 'L' and resid 155 through 161 Processing helix chain 'L' and resid 173 through 185 removed outlier: 3.934A pdb=" N ILE L 180 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG L 183 " --> pdb=" O SER L 179 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER L 185 " --> pdb=" O LEU L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 242 Processing helix chain 'L' and resid 248 through 269 removed outlier: 3.824A pdb=" N ASN L 252 " --> pdb=" O GLY L 248 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE L 255 " --> pdb=" O ARG L 251 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASP L 256 " --> pdb=" O ASN L 252 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU L 266 " --> pdb=" O LYS L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 299 Processing helix chain 'L' and resid 311 through 315 Processing helix chain 'L' and resid 360 through 373 removed outlier: 3.632A pdb=" N GLU L 365 " --> pdb=" O ARG L 361 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS L 372 " --> pdb=" O ALA L 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 381 Processing helix chain 'L' and resid 396 through 405 removed outlier: 3.589A pdb=" N LEU L 400 " --> pdb=" O ASP L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 423 through 441 removed outlier: 3.591A pdb=" N ILE L 428 " --> pdb=" O LEU L 424 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE L 432 " --> pdb=" O ILE L 428 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG L 433 " --> pdb=" O GLY L 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 472 through 488 removed outlier: 6.232A pdb=" N ARG L 485 " --> pdb=" O VAL L 481 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LYS L 486 " --> pdb=" O LYS L 482 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR L 487 " --> pdb=" O GLU L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 501 Processing helix chain 'L' and resid 502 through 507 removed outlier: 3.704A pdb=" N SER L 507 " --> pdb=" O SER L 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 527 removed outlier: 3.544A pdb=" N ARG L 523 " --> pdb=" O ASN L 519 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS L 525 " --> pdb=" O SER L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 579 through 585 Processing helix chain 'L' and resid 592 through 603 removed outlier: 4.365A pdb=" N VAL L 596 " --> pdb=" O ASP L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 656 through 658 No H-bonds generated for 'chain 'L' and resid 656 through 658' Processing helix chain 'L' and resid 667 through 676 removed outlier: 3.669A pdb=" N THR L 671 " --> pdb=" O GLU L 667 " (cutoff:3.500A) Processing helix chain 'L' and resid 682 through 687 Processing sheet with id=AA1, first strand: chain 'D' and resid 17 through 20 removed outlier: 6.369A pdb=" N ARG D 26 " --> pdb=" O GLN D 18 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 28 current: chain 'D' and resid 61 through 70 removed outlier: 7.337A pdb=" N ASN D 62 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU D 97 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE D 64 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER D 91 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL D 70 " --> pdb=" O TRP D 89 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TRP D 89 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 150 through 154 removed outlier: 4.691A pdb=" N GLY D 141 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL D 153 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER D 139 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN D 142 " --> pdb=" O ILE D 563 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA D 164 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU D 493 " --> pdb=" O SER D 163 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D 458 " --> pdb=" O VAL D 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 195 through 197 removed outlier: 3.523A pdb=" N SER D 412 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS D 213 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU D 224 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS D 216 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 15 through 21 removed outlier: 6.872A pdb=" N ARG M 26 " --> pdb=" O GLN M 18 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL M 20 " --> pdb=" O ASN M 24 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN M 24 " --> pdb=" O VAL M 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 104 through 106 removed outlier: 3.544A pdb=" N GLY M 96 " --> pdb=" O PHE M 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE M 64 " --> pdb=" O GLY M 96 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASN M 62 " --> pdb=" O GLU M 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'M' and resid 141 through 143 removed outlier: 6.371A pdb=" N ALA M 164 " --> pdb=" O PHE M 513 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL M 456 " --> pdb=" O GLY M 490 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL M 197 " --> pdb=" O PHE M 414 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS M 213 " --> pdb=" O ILE M 411 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU M 224 " --> pdb=" O VAL M 214 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS M 216 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 617 through 618 removed outlier: 3.899A pdb=" N LEU M 617 " --> pdb=" O ILE M 641 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE M 641 " --> pdb=" O LEU M 617 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER M 640 " --> pdb=" O GLU M 653 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'N' and resid 97 through 98 removed outlier: 3.608A pdb=" N GLU N 105 " --> pdb=" O GLU N 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 151 through 154 removed outlier: 7.002A pdb=" N ALA N 151 " --> pdb=" O LEU N 140 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU N 493 " --> pdb=" O SER N 163 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL N 165 " --> pdb=" O LEU N 493 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER N 495 " --> pdb=" O VAL N 165 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE N 195 " --> pdb=" O SER N 412 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE N 414 " --> pdb=" O ILE N 195 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL N 197 " --> pdb=" O PHE N 414 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 617 through 618 removed outlier: 3.738A pdb=" N SER N 640 " --> pdb=" O GLU N 653 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU N 653 " --> pdb=" O SER N 640 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR N 649 " --> pdb=" O GLU N 644 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU N 650 " --> pdb=" O TYR N 662 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU N 658 " --> pdb=" O PHE N 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 13 through 20 removed outlier: 4.995A pdb=" N THR O 16 " --> pdb=" O VAL O 28 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL O 28 " --> pdb=" O THR O 16 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ARG O 26 " --> pdb=" O GLN O 18 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 25 through 28 current: chain 'O' and resid 61 through 70 removed outlier: 6.826A pdb=" N ASN O 62 " --> pdb=" O GLU O 97 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU O 97 " --> pdb=" O ASN O 62 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE O 64 " --> pdb=" O VAL O 95 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER O 91 " --> pdb=" O SER O 68 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL O 70 " --> pdb=" O TRP O 89 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TRP O 89 " --> pdb=" O VAL O 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 104 through 106 current: chain 'L' and resid 61 through 71 removed outlier: 6.976A pdb=" N ASN L 62 " --> pdb=" O GLU L 97 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU L 97 " --> pdb=" O ASN L 62 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE L 64 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER L 91 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 150 through 154 removed outlier: 5.927A pdb=" N ALA O 151 " --> pdb=" O LEU O 140 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN O 142 " --> pdb=" O ILE O 563 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA O 164 " --> pdb=" O PHE O 513 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU O 458 " --> pdb=" O VAL O 494 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 198 through 199 removed outlier: 5.965A pdb=" N LYS O 213 " --> pdb=" O ILE O 413 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP O 415 " --> pdb=" O LYS O 213 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR O 215 " --> pdb=" O ASP O 415 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 617 through 618 removed outlier: 3.792A pdb=" N LEU O 617 " --> pdb=" O ILE O 641 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER O 640 " --> pdb=" O GLU O 653 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU O 653 " --> pdb=" O SER O 640 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 15 through 20 removed outlier: 3.669A pdb=" N GLN L 18 " --> pdb=" O ARG L 26 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG L 26 " --> pdb=" O GLN L 18 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 150 through 154 removed outlier: 4.186A pdb=" N GLY L 141 " --> pdb=" O ALA L 151 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL L 153 " --> pdb=" O SER L 139 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N SER L 139 " --> pdb=" O VAL L 153 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA L 164 " --> pdb=" O PHE L 513 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU L 454 " --> pdb=" O GLY L 490 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N MET L 492 " --> pdb=" O LEU L 454 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL L 456 " --> pdb=" O MET L 492 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL L 494 " --> pdb=" O VAL L 456 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU L 458 " --> pdb=" O VAL L 494 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE L 413 " --> pdb=" O LYS L 213 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU L 224 " --> pdb=" O ALA L 212 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL L 214 " --> pdb=" O LEU L 224 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 616 through 618 removed outlier: 3.516A pdb=" N SER L 640 " --> pdb=" O GLU L 653 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 653 " --> pdb=" O SER L 640 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 662 through 663 removed outlier: 4.201A pdb=" N ARG L 692 " --> pdb=" O TYR L 663 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 1938 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: 4.42 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7536 1.36 - 1.50: 5736 1.50 - 1.64: 9655 1.64 - 1.78: 24 1.78 - 1.91: 97 Bond restraints: 23048 Sorted by residual: bond pdb=" C1' AGS M 701 " pdb=" C2' AGS M 701 " ideal model delta sigma weight residual 1.544 1.275 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C1' AGS L 701 " pdb=" C2' AGS L 701 " ideal model delta sigma weight residual 1.544 1.277 0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C1' AGS O 701 " pdb=" C2' AGS O 701 " ideal model delta sigma weight residual 1.544 1.279 0.265 2.00e-02 2.50e+03 1.75e+02 bond pdb=" C3' AGS M 701 " pdb=" C4' AGS M 701 " ideal model delta sigma weight residual 1.530 1.272 0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C3' AGS L 701 " pdb=" C4' AGS L 701 " ideal model delta sigma weight residual 1.530 1.274 0.256 2.00e-02 2.50e+03 1.64e+02 ... (remaining 23043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 30971 2.59 - 5.17: 240 5.17 - 7.76: 29 7.76 - 10.34: 14 10.34 - 12.93: 12 Bond angle restraints: 31266 Sorted by residual: angle pdb=" O1A AGS L 701 " pdb=" PA AGS L 701 " pdb=" O2A AGS L 701 " ideal model delta sigma weight residual 122.09 109.16 12.93 3.00e+00 1.11e-01 1.86e+01 angle pdb=" O1A AGS O 701 " pdb=" PA AGS O 701 " pdb=" O2A AGS O 701 " ideal model delta sigma weight residual 122.09 109.20 12.89 3.00e+00 1.11e-01 1.85e+01 angle pdb=" O1A AGS M 701 " pdb=" PA AGS M 701 " pdb=" O2A AGS M 701 " ideal model delta sigma weight residual 122.09 109.36 12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O3A AGS O 701 " pdb=" PA AGS O 701 " pdb=" O5' AGS O 701 " ideal model delta sigma weight residual 97.67 110.31 -12.64 3.00e+00 1.11e-01 1.78e+01 angle pdb=" O1B AGS M 701 " pdb=" PB AGS M 701 " pdb=" O2B AGS M 701 " ideal model delta sigma weight residual 121.53 109.21 12.32 3.00e+00 1.11e-01 1.69e+01 ... (remaining 31261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.48: 13013 20.48 - 40.97: 797 40.97 - 61.45: 80 61.45 - 81.93: 31 81.93 - 102.41: 14 Dihedral angle restraints: 13935 sinusoidal: 5453 harmonic: 8482 Sorted by residual: dihedral pdb=" CA LYS N 486 " pdb=" C LYS N 486 " pdb=" N TYR N 487 " pdb=" CA TYR N 487 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ARG L 161 " pdb=" C ARG L 161 " pdb=" N HIS L 162 " pdb=" CA HIS L 162 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA HIS L 679 " pdb=" C HIS L 679 " pdb=" N GLY L 680 " pdb=" CA GLY L 680 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 13932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3131 0.061 - 0.122: 463 0.122 - 0.182: 39 0.182 - 0.243: 0 0.243 - 0.304: 3 Chirality restraints: 3636 Sorted by residual: chirality pdb=" C2' AGS O 701 " pdb=" C1' AGS O 701 " pdb=" C3' AGS O 701 " pdb=" O2' AGS O 701 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C2' AGS L 701 " pdb=" C1' AGS L 701 " pdb=" C3' AGS L 701 " pdb=" O2' AGS L 701 " both_signs ideal model delta sigma weight residual False -2.73 -2.44 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' AGS M 701 " pdb=" C1' AGS M 701 " pdb=" C3' AGS M 701 " pdb=" O2' AGS M 701 " both_signs ideal model delta sigma weight residual False -2.73 -2.45 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 3633 not shown) Planarity restraints: 3983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 89 " 0.019 2.00e-02 2.50e+03 2.19e-02 1.20e+01 pdb=" CG TRP D 89 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP D 89 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP D 89 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 89 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP D 89 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 89 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 89 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 89 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP D 89 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 218 " 0.054 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO L 219 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO L 219 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 219 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP N 373 " 0.046 5.00e-02 4.00e+02 7.07e-02 8.01e+00 pdb=" N PRO N 374 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO N 374 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO N 374 " 0.039 5.00e-02 4.00e+02 ... (remaining 3980 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 285 2.56 - 3.15: 19554 3.15 - 3.73: 32496 3.73 - 4.31: 44932 4.31 - 4.90: 75515 Nonbonded interactions: 172782 Sorted by model distance: nonbonded pdb=" O3G AGS M 701 " pdb="MG MG M 702 " model vdw 1.975 2.170 nonbonded pdb=" OH TYR O 297 " pdb=" O LEU O 364 " model vdw 2.002 3.040 nonbonded pdb=" O2G AGS L 701 " pdb="MG MG L 702 " model vdw 2.031 2.170 nonbonded pdb=" O PHE M 682 " pdb=" OG SER M 685 " model vdw 2.034 3.040 nonbonded pdb=" O ALA N 232 " pdb=" NH2 ARG N 433 " model vdw 2.045 3.120 ... (remaining 172777 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 'L' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 28 or (resid 29 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 55 or (resid 56 and (name N or na \ me CA or name C or name O or name CB )) or resid 57 through 59 or (resid 60 and \ (name N or name CA or name C or name O or name CB )) or resid 61 through 67 or ( \ resid 68 through 69 and (name N or name CA or name C or name O or name CB )) or \ resid 70 through 77 or (resid 78 and (name N or name CA or name C or name O or n \ ame CB )) or resid 79 through 80 or (resid 81 through 83 and (name N or name CA \ or name C or name O or name CB )) or resid 84 or (resid 85 and (name N or name C \ A or name C or name O or name CB )) or resid 86 or (resid 87 through 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 through 98 and (name N or name CA or name C or name O or name CB )) or resi \ d 99 or (resid 100 through 106 and (name N or name CA or name C or name O or nam \ e CB )) or resid 107 through 109 or (resid 110 and (name N or name CA or name C \ or name O or name CB )) or resid 111 through 122 or (resid 123 and (name N or na \ me CA or name C or name O or name CB )) or resid 124 or (resid 125 and (name N o \ r name CA or name C or name O or name CB )) or resid 126 through 129 or (resid 1 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 155 or (resid 156 and (name N or name CA or name C or name O or name CB )) or r \ esid 157 through 316 or resid 331 through 364 or (resid 365 and (name N or name \ CA or name C or name O or name CB )) or resid 366 through 446 or (resid 447 and \ (name N or name CA or name C or name O or name CB )) or resid 448 through 521 or \ (resid 522 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 3 through 534 or (resid 535 and (name N or name CA or name C or name O or name C \ B )) or resid 536 through 547 or (resid 548 through 549 and (name N or name CA o \ r name C or name O or name CB )) or resid 550 through 570 or (resid 571 and (nam \ e N or name CA or name C or name O or name CB )) or resid 572 through 637 or (re \ sid 638 and (name N or name CA or name C or name O or name CB )) or resid 639 th \ rough 651 or (resid 652 through 656 and (name N or name CA or name C or name O o \ r name CB )) or resid 657 or (resid 658 and (name N or name CA or name C or name \ O or name CB )) or resid 659 through 672 or (resid 673 and (name N or name CA o \ r name C or name O or name CB )) or resid 674 through 676 or (resid 677 through \ 679 and (name N or name CA or name C or name O or name CB )) or (resid 680 throu \ gh 683 and (name N or name CA or name C or name O or name CB )) or resid 684 thr \ ough 685 or (resid 686 and (name N or name CA or name C or name O or name CB )) \ or resid 687 through 702)) selection = (chain 'M' and (resid 11 through 67 or (resid 68 through 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 155 or (resid 156 and ( \ name N or name CA or name C or name O or name CB )) or resid 157 through 364 or \ (resid 365 and (name N or name CA or name C or name O or name CB )) or resid 366 \ through 446 or (resid 447 and (name N or name CA or name C or name O or name CB \ )) or resid 448 through 534 or (resid 535 and (name N or name CA or name C or n \ ame O or name CB )) or resid 536 through 547 or (resid 548 through 549 and (name \ N or name CA or name C or name O or name CB )) or resid 550 through 637 or (res \ id 638 and (name N or name CA or name C or name O or name CB )) or resid 639 thr \ ough 651 or (resid 652 through 656 and (name N or name CA or name C or name O or \ name CB )) or resid 657 or (resid 658 and (name N or name CA or name C or name \ O or name CB )) or resid 659 through 678 or (resid 679 and (name N or name CA or \ name C or name O or name CB )) or (resid 680 through 683 and (name N or name CA \ or name C or name O or name CB )) or resid 684 through 702)) selection = (chain 'O' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 28 or (resid 29 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 55 or (resid 56 and (name N or na \ me CA or name C or name O or name CB )) or resid 57 through 59 or (resid 60 and \ (name N or name CA or name C or name O or name CB )) or resid 61 through 77 or ( \ resid 78 and (name N or name CA or name C or name O or name CB )) or resid 79 th \ rough 80 or (resid 81 through 83 and (name N or name CA or name C or name O or n \ ame CB )) or resid 84 or (resid 85 and (name N or name CA or name C or name O or \ name CB )) or resid 86 or (resid 87 through 88 and (name N or name CA or name C \ or name O or name CB )) or resid 89 through 96 or (resid 97 through 98 and (nam \ e N or name CA or name C or name O or name CB )) or resid 99 or (resid 100 throu \ gh 106 and (name N or name CA or name C or name O or name CB )) or resid 107 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 122 or (resid 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 or (resid 125 and (name N or name CA or name C or n \ ame O or name CB )) or resid 126 through 129 or (resid 130 and (name N or name C \ A or name C or name O or name CB )) or resid 131 through 316 or resid 331 throug \ h 521 or (resid 522 and (name N or name CA or name C or name O or name CB )) or \ resid 523 through 672 or (resid 673 and (name N or name CA or name C or name O o \ r name CB )) or resid 674 through 676 or (resid 677 through 679 and (name N or n \ ame CA or name C or name O or name CB )) or resid 680 or (resid 681 through 683 \ and (name N or name CA or name C or name O or name CB )) or resid 684 through 68 \ 5 or (resid 686 and (name N or name CA or name C or name O or name CB )) or resi \ d 687 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 22.030 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 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 : 0.006 0.269 23048 Z= 0.307 Angle : 0.653 12.926 31266 Z= 0.320 Chirality : 0.044 0.304 3636 Planarity : 0.005 0.095 3983 Dihedral : 13.489 102.414 8487 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.52 % Favored : 94.44 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.67 % 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 are not related in a simple way. whole: -1.82 (0.15), residues: 2916 helix: -0.73 (0.18), residues: 836 sheet: -1.78 (0.26), residues: 400 loop : -1.28 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 375 TYR 0.012 0.001 TYR O 130 PHE 0.019 0.001 PHE O 534 TRP 0.055 0.002 TRP D 89 HIS 0.008 0.001 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.31 (23048) covalent geometry : angle 0.65310 / 0.32 (31266) hydrogen bonds : bond 0.27511 / 18.37 ( 698) hydrogen bonds : angle 9.72837 / 6.85 ( 1938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.5962 (pptt) cc_final: 0.5600 (mmtt) REVERT: D 263 LEU cc_start: 0.7876 (tp) cc_final: 0.7675 (pp) REVERT: D 437 ASP cc_start: 0.8022 (t0) cc_final: 0.7752 (t0) REVERT: M 217 VAL cc_start: 0.5974 (t) cc_final: 0.5761 (m) REVERT: M 491 MET cc_start: 0.7313 (tpp) cc_final: 0.6672 (tpp) REVERT: N 375 ARG cc_start: 0.4555 (tmt170) cc_final: 0.3660 (tpt90) REVERT: N 486 LYS cc_start: 0.6654 (pptt) cc_final: 0.6282 (pptt) REVERT: N 491 MET cc_start: 0.4081 (mpp) cc_final: 0.3861 (mpp) REVERT: N 492 MET cc_start: 0.7097 (tpt) cc_final: 0.6428 (ttt) REVERT: N 576 LEU cc_start: 0.6777 (mp) cc_final: 0.6075 (pp) REVERT: O 98 GLU cc_start: 0.6623 (tm-30) cc_final: 0.5860 (tm-30) REVERT: O 268 ARG cc_start: 0.7475 (ptp90) cc_final: 0.7117 (ptp-170) REVERT: O 480 ILE cc_start: 0.8450 (mt) cc_final: 0.8145 (mt) REVERT: L 266 LEU cc_start: 0.7253 (tt) cc_final: 0.6765 (mt) outliers start: 2 outliers final: 0 residues processed: 359 average time/residue: 0.1581 time to fit residues: 88.6136 Evaluate side-chains 254 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 290 HIS D 388 ASN M 119 HIS M 290 HIS M 670 HIS N 49 GLN N 381 ASN ** O 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 314 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.190117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.153266 restraints weight = 35874.448| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 3.70 r_work: 0.3855 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23048 Z= 0.157 Angle : 0.654 9.649 31266 Z= 0.336 Chirality : 0.049 0.181 3636 Planarity : 0.005 0.078 3983 Dihedral : 7.662 69.668 3299 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.12 % Allowed : 8.33 % Favored : 90.55 % 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 are not related in a simple way. whole: -1.56 (0.15), residues: 2916 helix: -0.44 (0.18), residues: 890 sheet: -1.48 (0.25), residues: 407 loop : -1.22 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 55 TYR 0.022 0.001 TYR O 85 PHE 0.016 0.002 PHE M 414 TRP 0.036 0.002 TRP D 89 HIS 0.009 0.001 HIS N 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (23048) covalent geometry : angle 0.65449 / 0.34 (31266) hydrogen bonds : bond 0.05087 / 3.39 ( 698) hydrogen bonds : angle 6.35667 / 4.42 ( 1938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.6259 (pptt) cc_final: 0.5691 (mmtp) REVERT: D 263 LEU cc_start: 0.7817 (tp) cc_final: 0.7580 (pp) REVERT: D 437 ASP cc_start: 0.8143 (t0) cc_final: 0.7740 (t0) REVERT: D 492 MET cc_start: 0.6588 (ttm) cc_final: 0.6308 (ttm) REVERT: D 508 GLN cc_start: 0.6088 (OUTLIER) cc_final: 0.5479 (mp10) REVERT: M 256 ASP cc_start: 0.7961 (t0) cc_final: 0.7743 (m-30) REVERT: M 381 ASN cc_start: 0.7526 (t0) cc_final: 0.7261 (t0) REVERT: M 419 MET cc_start: 0.7246 (mmm) cc_final: 0.7005 (mmp) REVERT: M 491 MET cc_start: 0.7553 (tpp) cc_final: 0.7115 (tpp) REVERT: M 492 MET cc_start: 0.7487 (tpp) cc_final: 0.7196 (tpp) REVERT: N 419 MET cc_start: 0.1923 (mmt) cc_final: 0.1708 (mmt) REVERT: N 478 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7091 (mtp180) REVERT: N 492 MET cc_start: 0.7865 (tpt) cc_final: 0.7255 (ttt) REVERT: N 576 LEU cc_start: 0.6740 (mp) cc_final: 0.6050 (pp) REVERT: N 644 GLU cc_start: 0.5838 (tt0) cc_final: 0.5392 (tt0) REVERT: N 651 GLU cc_start: 0.7229 (tt0) cc_final: 0.5816 (pm20) REVERT: O 98 GLU cc_start: 0.7353 (tm-30) cc_final: 0.6552 (tm-30) REVERT: O 126 LEU cc_start: 0.8152 (pp) cc_final: 0.7514 (tt) REVERT: O 268 ARG cc_start: 0.7635 (ptp90) cc_final: 0.6963 (ptp90) REVERT: O 362 LYS cc_start: 0.8221 (tmmt) cc_final: 0.7961 (ttpt) REVERT: O 480 ILE cc_start: 0.8059 (mt) cc_final: 0.7823 (mt) REVERT: O 600 TRP cc_start: 0.6504 (t60) cc_final: 0.5545 (t60) REVERT: L 485 ARG cc_start: 0.8797 (ttt-90) cc_final: 0.8546 (ptm160) REVERT: L 497 ARG cc_start: 0.8513 (tpt90) cc_final: 0.8180 (tpt90) outliers start: 27 outliers final: 17 residues processed: 323 average time/residue: 0.1690 time to fit residues: 83.1351 Evaluate side-chains 267 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 249 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain M residue 188 SER Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain M residue 518 ASN Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain L residue 125 ASP Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 684 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 145 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 169 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 18 GLN D 62 ASN N 49 GLN N 381 ASN O 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.188544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.151612 restraints weight = 35982.794| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.63 r_work: 0.3836 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23048 Z= 0.153 Angle : 0.607 12.566 31266 Z= 0.309 Chirality : 0.047 0.186 3636 Planarity : 0.004 0.073 3983 Dihedral : 6.827 69.628 3299 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.96 % Allowed : 12.62 % Favored : 85.42 % 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 are not related in a simple way. whole: -1.48 (0.15), residues: 2916 helix: -0.34 (0.18), residues: 895 sheet: -1.38 (0.25), residues: 416 loop : -1.21 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 450 TYR 0.018 0.001 TYR O 85 PHE 0.015 0.002 PHE L 198 TRP 0.016 0.002 TRP D 89 HIS 0.026 0.002 HIS D 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (23048) covalent geometry : angle 0.60738 / 0.31 (31266) hydrogen bonds : bond 0.04363 / 2.95 ( 698) hydrogen bonds : angle 5.87589 / 4.09 ( 1938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 266 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.6422 (pptt) cc_final: 0.5759 (mmtp) REVERT: M 256 ASP cc_start: 0.8039 (t0) cc_final: 0.7777 (m-30) REVERT: M 381 ASN cc_start: 0.7662 (t0) cc_final: 0.7320 (t0) REVERT: M 491 MET cc_start: 0.7480 (tpp) cc_final: 0.7123 (tpp) REVERT: N 225 LYS cc_start: 0.7860 (pttp) cc_final: 0.7508 (pptt) REVERT: N 297 TYR cc_start: 0.2016 (m-80) cc_final: 0.1723 (m-80) REVERT: N 419 MET cc_start: 0.2807 (mmt) cc_final: 0.2400 (mmt) REVERT: N 437 ASP cc_start: 0.5811 (m-30) cc_final: 0.5154 (p0) REVERT: N 492 MET cc_start: 0.7876 (tpt) cc_final: 0.7341 (ttt) REVERT: N 576 LEU cc_start: 0.6628 (mp) cc_final: 0.5963 (pp) REVERT: N 651 GLU cc_start: 0.7376 (tt0) cc_final: 0.5693 (pm20) REVERT: O 98 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6679 (tm-30) REVERT: O 126 LEU cc_start: 0.8043 (pp) cc_final: 0.7402 (tt) REVERT: O 261 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7481 (mp) REVERT: O 362 LYS cc_start: 0.8365 (tmmt) cc_final: 0.8022 (ttpp) REVERT: O 480 ILE cc_start: 0.7922 (mt) cc_final: 0.7603 (mt) REVERT: O 600 TRP cc_start: 0.6502 (t60) cc_final: 0.5932 (t60) REVERT: L 69 GLN cc_start: 0.8317 (mt0) cc_final: 0.7821 (mp-120) REVERT: L 497 ARG cc_start: 0.8402 (tpt90) cc_final: 0.8103 (tpt90) outliers start: 47 outliers final: 25 residues processed: 303 average time/residue: 0.1641 time to fit residues: 76.9604 Evaluate side-chains 264 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 188 SER Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain M residue 518 ASN Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain O residue 261 LEU Chi-restraints excluded: chain O residue 469 SER Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 684 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 262 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 154 optimal weight: 0.0270 overall best weight: 3.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 444 ASN N 49 GLN N 162 HIS N 381 ASN L 290 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.184656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.145646 restraints weight = 36415.744| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 3.36 r_work: 0.3805 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23048 Z= 0.211 Angle : 0.669 11.117 31266 Z= 0.342 Chirality : 0.049 0.226 3636 Planarity : 0.005 0.068 3983 Dihedral : 6.845 74.426 3299 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.96 % Allowed : 15.33 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.15), residues: 2916 helix: -0.53 (0.17), residues: 896 sheet: -1.38 (0.25), residues: 414 loop : -1.35 (0.14), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 616 TYR 0.027 0.002 TYR O 130 PHE 0.021 0.002 PHE L 378 TRP 0.025 0.002 TRP N 600 HIS 0.013 0.002 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (23048) covalent geometry : angle 0.66898 / 0.34 (31266) hydrogen bonds : bond 0.04559 / 3.10 ( 698) hydrogen bonds : angle 5.80791 / 4.05 ( 1938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 260 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 98 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7652 (tm-30) REVERT: D 508 GLN cc_start: 0.6067 (OUTLIER) cc_final: 0.5568 (mp10) REVERT: M 187 MET cc_start: 0.7222 (mmm) cc_final: 0.6996 (mmm) REVERT: M 256 ASP cc_start: 0.8045 (t0) cc_final: 0.7775 (m-30) REVERT: M 381 ASN cc_start: 0.7787 (t0) cc_final: 0.7397 (t0) REVERT: M 434 ILE cc_start: 0.7351 (mt) cc_final: 0.6909 (mt) REVERT: M 436 TYR cc_start: 0.6495 (t80) cc_final: 0.6263 (t80) REVERT: M 447 GLU cc_start: 0.6293 (pp20) cc_final: 0.5264 (pp20) REVERT: M 491 MET cc_start: 0.7371 (tpp) cc_final: 0.6886 (tpp) REVERT: N 215 TYR cc_start: 0.5476 (m-80) cc_final: 0.5227 (m-80) REVERT: N 225 LYS cc_start: 0.7962 (pttp) cc_final: 0.7538 (pptt) REVERT: N 269 GLN cc_start: 0.5221 (tp-100) cc_final: 0.4662 (tm-30) REVERT: N 297 TYR cc_start: 0.2705 (m-80) cc_final: 0.2348 (m-80) REVERT: N 419 MET cc_start: 0.3339 (mmt) cc_final: 0.3002 (mmm) REVERT: N 437 ASP cc_start: 0.5779 (m-30) cc_final: 0.5154 (p0) REVERT: N 492 MET cc_start: 0.7773 (tpt) cc_final: 0.7312 (ttt) REVERT: N 560 MET cc_start: 0.5093 (pmm) cc_final: 0.3915 (mtm) REVERT: N 576 LEU cc_start: 0.6817 (mp) cc_final: 0.6008 (pp) REVERT: N 651 GLU cc_start: 0.7365 (tt0) cc_final: 0.5724 (pm20) REVERT: O 98 GLU cc_start: 0.7636 (tm-30) cc_final: 0.6916 (tm-30) REVERT: O 215 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.7064 (m-10) REVERT: O 480 ILE cc_start: 0.7919 (mt) cc_final: 0.7697 (mt) REVERT: O 497 ARG cc_start: 0.7384 (ttm-80) cc_final: 0.6935 (tpt170) REVERT: O 579 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6610 (p0) REVERT: O 600 TRP cc_start: 0.6434 (t60) cc_final: 0.5793 (t60) REVERT: L 69 GLN cc_start: 0.8304 (mt0) cc_final: 0.7856 (mp-120) REVERT: L 497 ARG cc_start: 0.8348 (tpt90) cc_final: 0.8025 (tpt90) REVERT: L 545 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7167 (ttm110) outliers start: 71 outliers final: 41 residues processed: 314 average time/residue: 0.1556 time to fit residues: 76.3705 Evaluate side-chains 281 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 174 SER Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain M residue 501 ILE Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 518 ASN Chi-restraints excluded: chain M residue 556 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 215 TYR Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain O residue 469 SER Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 534 PHE Chi-restraints excluded: chain O residue 579 ASP Chi-restraints excluded: chain O residue 650 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 501 ILE Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 545 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 0.5980 chunk 285 optimal weight: 0.9990 chunk 2 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 251 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 126 optimal weight: 0.5980 chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 381 ASN N 679 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.189367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.152865 restraints weight = 35686.028| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 3.74 r_work: 0.3851 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23048 Z= 0.108 Angle : 0.564 9.450 31266 Z= 0.287 Chirality : 0.046 0.205 3636 Planarity : 0.004 0.065 3983 Dihedral : 6.239 59.768 3299 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.92 % Allowed : 16.87 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 2916 helix: -0.26 (0.18), residues: 905 sheet: -1.25 (0.26), residues: 392 loop : -1.18 (0.14), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 606 TYR 0.010 0.001 TYR O 130 PHE 0.019 0.001 PHE L 378 TRP 0.048 0.002 TRP N 600 HIS 0.011 0.001 HIS N 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (23048) covalent geometry : angle 0.56382 / 0.29 (31266) hydrogen bonds : bond 0.03503 / 2.40 ( 698) hydrogen bonds : angle 5.43989 / 3.80 ( 1938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: D 98 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7328 (tm-30) REVERT: D 133 GLN cc_start: 0.8291 (mt0) cc_final: 0.7730 (pp30) REVERT: D 135 LYS cc_start: 0.6565 (pptt) cc_final: 0.6063 (mmtp) REVERT: D 452 ARG cc_start: 0.6443 (ttp80) cc_final: 0.5593 (mtp85) REVERT: M 256 ASP cc_start: 0.7996 (t70) cc_final: 0.7709 (m-30) REVERT: M 263 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6900 (mt) REVERT: M 381 ASN cc_start: 0.7740 (t0) cc_final: 0.7312 (t0) REVERT: M 491 MET cc_start: 0.7327 (tpp) cc_final: 0.6929 (tpp) REVERT: N 225 LYS cc_start: 0.8059 (pttp) cc_final: 0.7821 (pptt) REVERT: N 297 TYR cc_start: 0.2613 (m-80) cc_final: 0.2316 (m-80) REVERT: N 375 ARG cc_start: 0.4460 (OUTLIER) cc_final: 0.3142 (tpt90) REVERT: N 419 MET cc_start: 0.3354 (mmt) cc_final: 0.2961 (mmt) REVERT: N 437 ASP cc_start: 0.6087 (m-30) cc_final: 0.5476 (p0) REVERT: N 492 MET cc_start: 0.7643 (tpt) cc_final: 0.7378 (ttt) REVERT: N 560 MET cc_start: 0.4762 (pmm) cc_final: 0.3939 (mtt) REVERT: N 576 LEU cc_start: 0.6800 (mp) cc_final: 0.5984 (pp) REVERT: N 651 GLU cc_start: 0.7335 (tt0) cc_final: 0.5648 (pm20) REVERT: O 24 ASN cc_start: 0.7628 (t0) cc_final: 0.7351 (m110) REVERT: O 98 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6800 (tm-30) REVERT: O 126 LEU cc_start: 0.7994 (pp) cc_final: 0.7351 (tt) REVERT: O 338 ILE cc_start: 0.7787 (mp) cc_final: 0.7310 (tp) REVERT: O 497 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6674 (ttm-80) REVERT: O 579 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6578 (p0) REVERT: O 600 TRP cc_start: 0.6494 (t60) cc_final: 0.5924 (t60) REVERT: L 66 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6635 (mm) REVERT: L 69 GLN cc_start: 0.8213 (mt0) cc_final: 0.7779 (mp-120) REVERT: L 79 LEU cc_start: 0.7211 (tt) cc_final: 0.6581 (mp) REVERT: L 80 LEU cc_start: 0.5983 (OUTLIER) cc_final: 0.5727 (tt) REVERT: L 361 ARG cc_start: 0.6107 (tpt170) cc_final: 0.4716 (mmm160) REVERT: L 497 ARG cc_start: 0.8281 (tpt90) cc_final: 0.8013 (tpt90) outliers start: 46 outliers final: 26 residues processed: 310 average time/residue: 0.1582 time to fit residues: 77.2366 Evaluate side-chains 267 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 174 SER Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 278 SER Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain M residue 518 ASN Chi-restraints excluded: chain M residue 556 VAL Chi-restraints excluded: chain M residue 670 HIS Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 375 ARG Chi-restraints excluded: chain N residue 494 VAL Chi-restraints excluded: chain N residue 672 GLU Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 534 PHE Chi-restraints excluded: chain O residue 579 ASP Chi-restraints excluded: chain O residue 650 LEU Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 517 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 225 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN N 49 GLN N 656 HIS O 314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.180660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.141412 restraints weight = 36463.237| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 3.41 r_work: 0.3756 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 23048 Z= 0.305 Angle : 0.782 10.692 31266 Z= 0.399 Chirality : 0.052 0.242 3636 Planarity : 0.006 0.064 3983 Dihedral : 7.239 74.365 3299 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.04 % Allowed : 16.87 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.15), residues: 2916 helix: -0.82 (0.17), residues: 888 sheet: -1.61 (0.25), residues: 407 loop : -1.49 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 616 TYR 0.032 0.002 TYR O 215 PHE 0.027 0.003 PHE L 440 TRP 0.090 0.003 TRP N 600 HIS 0.013 0.002 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.31 (23048) covalent geometry : angle 0.78231 / 0.40 (31266) hydrogen bonds : bond 0.05139 / 3.47 ( 698) hydrogen bonds : angle 5.93647 / 4.17 ( 1938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 246 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8092 (t) cc_final: 0.7297 (m) REVERT: D 98 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7374 (tm-30) REVERT: D 133 GLN cc_start: 0.8220 (mt0) cc_final: 0.7942 (pp30) REVERT: D 452 ARG cc_start: 0.6925 (ttp80) cc_final: 0.5936 (mtp85) REVERT: D 517 MET cc_start: 0.6614 (ttm) cc_final: 0.6061 (ttm) REVERT: D 538 MET cc_start: 0.4918 (ttm) cc_final: 0.4655 (ttm) REVERT: M 90 ILE cc_start: 0.2802 (OUTLIER) cc_final: 0.2344 (pt) REVERT: M 162 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.6725 (m90) REVERT: M 381 ASN cc_start: 0.7909 (t0) cc_final: 0.7477 (t0) REVERT: M 491 MET cc_start: 0.7485 (tpp) cc_final: 0.6875 (tpp) REVERT: N 225 LYS cc_start: 0.7924 (pttp) cc_final: 0.7705 (pptt) REVERT: N 269 GLN cc_start: 0.4770 (tp-100) cc_final: 0.4469 (tm-30) REVERT: N 375 ARG cc_start: 0.4309 (OUTLIER) cc_final: 0.2733 (tpt90) REVERT: N 419 MET cc_start: 0.3718 (mmt) cc_final: 0.2947 (mmt) REVERT: N 492 MET cc_start: 0.7805 (tpt) cc_final: 0.7269 (ttm) REVERT: N 651 GLU cc_start: 0.7395 (tt0) cc_final: 0.5728 (pm20) REVERT: O 98 GLU cc_start: 0.7666 (tm-30) cc_final: 0.6958 (tm-30) REVERT: O 497 ARG cc_start: 0.7508 (ttm-80) cc_final: 0.6912 (tpt170) REVERT: O 579 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6766 (p0) REVERT: O 600 TRP cc_start: 0.6440 (t60) cc_final: 0.5659 (t60) REVERT: L 69 GLN cc_start: 0.8438 (mt0) cc_final: 0.8021 (mp-120) REVERT: L 80 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5863 (tt) REVERT: L 88 ARG cc_start: 0.6890 (mmt180) cc_final: 0.6680 (mmt180) REVERT: L 152 LEU cc_start: 0.8314 (mt) cc_final: 0.8105 (mp) REVERT: L 497 ARG cc_start: 0.8476 (tpt90) cc_final: 0.8230 (tpt90) outliers start: 97 outliers final: 59 residues processed: 326 average time/residue: 0.1545 time to fit residues: 79.8071 Evaluate side-chains 287 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 223 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 551 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 162 HIS Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 188 SER Chi-restraints excluded: chain M residue 195 ILE Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain M residue 501 ILE Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 518 ASN Chi-restraints excluded: chain M residue 556 VAL Chi-restraints excluded: chain M residue 665 VAL Chi-restraints excluded: chain M residue 670 HIS Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 375 ARG Chi-restraints excluded: chain N residue 605 VAL Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain N residue 672 GLU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 218 THR Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain O residue 254 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 469 SER Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 534 PHE Chi-restraints excluded: chain O residue 579 ASP Chi-restraints excluded: chain O residue 650 LEU Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 526 VAL Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 684 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 3 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 314 ASN N 49 GLN O 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.186459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.143343 restraints weight = 35937.167| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 3.57 r_work: 0.3812 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23048 Z= 0.128 Angle : 0.610 9.271 31266 Z= 0.310 Chirality : 0.047 0.203 3636 Planarity : 0.004 0.060 3983 Dihedral : 6.424 63.042 3299 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.50 % Allowed : 18.91 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 2916 helix: -0.45 (0.17), residues: 912 sheet: -1.51 (0.25), residues: 397 loop : -1.28 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 601 TYR 0.010 0.001 TYR L 215 PHE 0.030 0.001 PHE O 378 TRP 0.066 0.002 TRP N 600 HIS 0.011 0.001 HIS N 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (23048) covalent geometry : angle 0.61034 / 0.31 (31266) hydrogen bonds : bond 0.03758 / 2.57 ( 698) hydrogen bonds : angle 5.50153 / 3.86 ( 1938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 249 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: D 52 SER cc_start: 0.8124 (t) cc_final: 0.7323 (m) REVERT: D 98 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7251 (tm-30) REVERT: D 133 GLN cc_start: 0.8278 (mt0) cc_final: 0.7767 (pp30) REVERT: D 135 LYS cc_start: 0.6752 (pptt) cc_final: 0.6280 (mmtp) REVERT: D 385 TRP cc_start: 0.6821 (m-90) cc_final: 0.6574 (m-90) REVERT: D 452 ARG cc_start: 0.6656 (ttp80) cc_final: 0.5760 (mtp85) REVERT: D 491 MET cc_start: 0.7679 (mmm) cc_final: 0.7125 (mmm) REVERT: D 517 MET cc_start: 0.6414 (ttm) cc_final: 0.5852 (ttm) REVERT: M 256 ASP cc_start: 0.7721 (t0) cc_final: 0.7428 (m-30) REVERT: M 381 ASN cc_start: 0.7755 (t0) cc_final: 0.7285 (t0) REVERT: M 441 TRP cc_start: 0.7352 (m100) cc_final: 0.7099 (m100) REVERT: M 491 MET cc_start: 0.7399 (tpp) cc_final: 0.7021 (tpp) REVERT: N 269 GLN cc_start: 0.4703 (tp-100) cc_final: 0.4254 (tm-30) REVERT: N 375 ARG cc_start: 0.4057 (OUTLIER) cc_final: 0.2637 (tpt90) REVERT: N 419 MET cc_start: 0.3613 (mmt) cc_final: 0.2922 (mmt) REVERT: N 437 ASP cc_start: 0.6020 (m-30) cc_final: 0.5374 (p0) REVERT: N 458 LEU cc_start: 0.4712 (pp) cc_final: 0.4471 (pt) REVERT: N 560 MET cc_start: 0.5112 (pmm) cc_final: 0.3518 (mtm) REVERT: N 576 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.5873 (pp) REVERT: N 651 GLU cc_start: 0.7435 (tt0) cc_final: 0.6108 (pm20) REVERT: O 24 ASN cc_start: 0.7769 (t0) cc_final: 0.7397 (m110) REVERT: O 98 GLU cc_start: 0.7641 (tm-30) cc_final: 0.6897 (tm-30) REVERT: O 497 ARG cc_start: 0.7107 (ttm-80) cc_final: 0.6523 (tpt170) REVERT: O 579 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6621 (p0) REVERT: O 600 TRP cc_start: 0.6557 (t60) cc_final: 0.5834 (t60) REVERT: O 651 GLU cc_start: 0.4754 (pp20) cc_final: 0.3476 (pt0) REVERT: L 66 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6552 (mm) REVERT: L 69 GLN cc_start: 0.8409 (mt0) cc_final: 0.8191 (mt0) REVERT: L 79 LEU cc_start: 0.7164 (tt) cc_final: 0.6620 (mp) REVERT: L 80 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5834 (tt) REVERT: L 361 ARG cc_start: 0.6573 (tpt170) cc_final: 0.5304 (mmm160) REVERT: L 497 ARG cc_start: 0.8385 (tpt90) cc_final: 0.8060 (tpt90) outliers start: 60 outliers final: 34 residues processed: 302 average time/residue: 0.1459 time to fit residues: 69.7836 Evaluate side-chains 272 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 551 ILE Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 278 SER Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 556 VAL Chi-restraints excluded: chain M residue 617 LEU Chi-restraints excluded: chain M residue 670 HIS Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 375 ARG Chi-restraints excluded: chain N residue 576 LEU Chi-restraints excluded: chain N residue 605 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 534 PHE Chi-restraints excluded: chain O residue 579 ASP Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 612 GLU Chi-restraints excluded: chain L residue 684 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 66 optimal weight: 2.9990 chunk 199 optimal weight: 20.0000 chunk 162 optimal weight: 8.9990 chunk 277 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 314 ASN M 444 ASN N 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.183421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.144187 restraints weight = 36297.067| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.43 r_work: 0.3786 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23048 Z= 0.199 Angle : 0.668 10.003 31266 Z= 0.339 Chirality : 0.048 0.194 3636 Planarity : 0.005 0.055 3983 Dihedral : 6.541 58.807 3299 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.04 % Allowed : 18.78 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.15), residues: 2916 helix: -0.51 (0.17), residues: 902 sheet: -1.52 (0.25), residues: 399 loop : -1.38 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 601 TYR 0.023 0.002 TYR O 130 PHE 0.022 0.002 PHE O 378 TRP 0.023 0.002 TRP N 600 HIS 0.013 0.002 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (23048) covalent geometry : angle 0.66850 / 0.34 (31266) hydrogen bonds : bond 0.04218 / 2.87 ( 698) hydrogen bonds : angle 5.61892 / 3.95 ( 1938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 238 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: D 52 SER cc_start: 0.8101 (t) cc_final: 0.7293 (m) REVERT: D 98 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7222 (tm-30) REVERT: D 133 GLN cc_start: 0.8264 (mt0) cc_final: 0.7811 (pp30) REVERT: D 135 LYS cc_start: 0.6720 (pptt) cc_final: 0.6365 (mmtp) REVERT: D 452 ARG cc_start: 0.6780 (ttp80) cc_final: 0.5871 (mtp85) REVERT: D 491 MET cc_start: 0.7697 (mmm) cc_final: 0.7195 (mmm) REVERT: D 517 MET cc_start: 0.6498 (ttm) cc_final: 0.5895 (ttm) REVERT: M 256 ASP cc_start: 0.7754 (t0) cc_final: 0.7503 (m-30) REVERT: M 381 ASN cc_start: 0.7839 (t0) cc_final: 0.7431 (t0) REVERT: M 441 TRP cc_start: 0.7435 (m100) cc_final: 0.7120 (m100) REVERT: M 491 MET cc_start: 0.7408 (tpp) cc_final: 0.6923 (tpp) REVERT: N 269 GLN cc_start: 0.4687 (tp-100) cc_final: 0.4262 (tm-30) REVERT: N 375 ARG cc_start: 0.4096 (OUTLIER) cc_final: 0.2615 (tpt90) REVERT: N 437 ASP cc_start: 0.6351 (m-30) cc_final: 0.5523 (p0) REVERT: N 576 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.5862 (pp) REVERT: N 648 MET cc_start: 0.2286 (tpp) cc_final: 0.2059 (tpp) REVERT: N 651 GLU cc_start: 0.7456 (tt0) cc_final: 0.5871 (pm20) REVERT: O 98 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6878 (tm-30) REVERT: O 464 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.7024 (m-80) REVERT: O 497 ARG cc_start: 0.7332 (ttm-80) cc_final: 0.6738 (tpt170) REVERT: O 579 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6734 (p0) REVERT: O 600 TRP cc_start: 0.6485 (t60) cc_final: 0.5737 (t60) REVERT: O 651 GLU cc_start: 0.4838 (pp20) cc_final: 0.3597 (pt0) REVERT: L 69 GLN cc_start: 0.8399 (mt0) cc_final: 0.8198 (mt0) REVERT: L 79 LEU cc_start: 0.7281 (tt) cc_final: 0.6646 (mp) REVERT: L 80 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5961 (tt) REVERT: L 152 LEU cc_start: 0.8198 (mt) cc_final: 0.7987 (mp) REVERT: L 361 ARG cc_start: 0.6482 (tpt170) cc_final: 0.5325 (mmm160) REVERT: L 367 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6569 (tp) REVERT: L 419 MET cc_start: 0.8413 (mmp) cc_final: 0.8156 (mmp) REVERT: L 482 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7325 (mttt) REVERT: L 497 ARG cc_start: 0.8372 (tpt90) cc_final: 0.8042 (tpt90) outliers start: 73 outliers final: 52 residues processed: 297 average time/residue: 0.1536 time to fit residues: 71.5076 Evaluate side-chains 285 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 226 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 551 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 278 SER Chi-restraints excluded: chain M residue 501 ILE Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 518 ASN Chi-restraints excluded: chain M residue 556 VAL Chi-restraints excluded: chain M residue 617 LEU Chi-restraints excluded: chain M residue 670 HIS Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 375 ARG Chi-restraints excluded: chain N residue 576 LEU Chi-restraints excluded: chain N residue 605 VAL Chi-restraints excluded: chain N residue 672 GLU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain O residue 254 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 464 TYR Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 534 PHE Chi-restraints excluded: chain O residue 579 ASP Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 367 LEU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 482 LYS Chi-restraints excluded: chain L residue 501 ILE Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 612 GLU Chi-restraints excluded: chain L residue 684 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 144 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 220 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN N 49 GLN O 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.183307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.144788 restraints weight = 36333.677| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.58 r_work: 0.3784 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23048 Z= 0.193 Angle : 0.674 10.485 31266 Z= 0.342 Chirality : 0.048 0.220 3636 Planarity : 0.005 0.058 3983 Dihedral : 6.289 54.093 3299 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.12 % Allowed : 19.08 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.15), residues: 2916 helix: -0.54 (0.17), residues: 909 sheet: -1.58 (0.25), residues: 413 loop : -1.41 (0.14), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 601 TYR 0.019 0.002 TYR O 130 PHE 0.025 0.002 PHE O 378 TRP 0.017 0.002 TRP O 89 HIS 0.011 0.002 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 (23048) covalent geometry : angle 0.67411 / 0.34 (31266) hydrogen bonds : bond 0.04100 / 2.78 ( 698) hydrogen bonds : angle 5.61930 / 3.96 ( 1938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 243 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: D 52 SER cc_start: 0.8062 (t) cc_final: 0.7253 (m) REVERT: D 133 GLN cc_start: 0.8322 (mt0) cc_final: 0.7862 (pp30) REVERT: D 135 LYS cc_start: 0.7015 (pptt) cc_final: 0.6535 (mmtp) REVERT: D 385 TRP cc_start: 0.6888 (m-90) cc_final: 0.6609 (m-90) REVERT: D 452 ARG cc_start: 0.6775 (ttp80) cc_final: 0.5926 (mtp85) REVERT: D 491 MET cc_start: 0.7601 (mmm) cc_final: 0.7129 (mmm) REVERT: D 517 MET cc_start: 0.6411 (ttm) cc_final: 0.5798 (ttm) REVERT: D 538 MET cc_start: 0.4717 (ttm) cc_final: 0.4402 (ttp) REVERT: M 256 ASP cc_start: 0.7817 (t0) cc_final: 0.7550 (m-30) REVERT: M 381 ASN cc_start: 0.7748 (t0) cc_final: 0.7317 (t0) REVERT: M 441 TRP cc_start: 0.7357 (m100) cc_final: 0.7082 (m100) REVERT: M 447 GLU cc_start: 0.6169 (pp20) cc_final: 0.4924 (pp20) REVERT: M 491 MET cc_start: 0.7378 (tpp) cc_final: 0.6961 (tpp) REVERT: N 225 LYS cc_start: 0.7773 (pptt) cc_final: 0.6174 (tttt) REVERT: N 269 GLN cc_start: 0.4675 (tp-100) cc_final: 0.4266 (tm-30) REVERT: N 375 ARG cc_start: 0.4117 (OUTLIER) cc_final: 0.2778 (tpt90) REVERT: N 437 ASP cc_start: 0.6342 (m-30) cc_final: 0.5473 (p0) REVERT: N 458 LEU cc_start: 0.4612 (pp) cc_final: 0.4357 (pt) REVERT: N 576 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5662 (pp) REVERT: N 608 GLN cc_start: 0.4763 (tm-30) cc_final: 0.4145 (mm-40) REVERT: N 648 MET cc_start: 0.2237 (tpp) cc_final: 0.1678 (tpp) REVERT: O 88 ARG cc_start: 0.6981 (ttp-170) cc_final: 0.6622 (tmm-80) REVERT: O 98 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6903 (tm-30) REVERT: O 464 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7052 (m-80) REVERT: O 497 ARG cc_start: 0.7354 (ttm-80) cc_final: 0.6818 (tpt170) REVERT: O 579 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6895 (p0) REVERT: O 600 TRP cc_start: 0.6603 (t60) cc_final: 0.5808 (t60) REVERT: O 651 GLU cc_start: 0.4770 (pp20) cc_final: 0.3574 (pt0) REVERT: L 79 LEU cc_start: 0.7325 (tt) cc_final: 0.6679 (mp) REVERT: L 152 LEU cc_start: 0.8216 (mt) cc_final: 0.8009 (mp) REVERT: L 361 ARG cc_start: 0.6546 (tpt170) cc_final: 0.5329 (mmm160) REVERT: L 419 MET cc_start: 0.8407 (mmp) cc_final: 0.8130 (mmp) REVERT: L 482 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7350 (mttt) REVERT: L 497 ARG cc_start: 0.8396 (tpt90) cc_final: 0.8062 (tpt90) outliers start: 75 outliers final: 57 residues processed: 307 average time/residue: 0.1616 time to fit residues: 77.8632 Evaluate side-chains 294 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 232 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 551 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 188 SER Chi-restraints excluded: chain M residue 195 ILE Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 501 ILE Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 556 VAL Chi-restraints excluded: chain M residue 617 LEU Chi-restraints excluded: chain M residue 670 HIS Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 375 ARG Chi-restraints excluded: chain N residue 439 LEU Chi-restraints excluded: chain N residue 576 LEU Chi-restraints excluded: chain N residue 605 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain O residue 254 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 464 TYR Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 534 PHE Chi-restraints excluded: chain O residue 579 ASP Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 234 THR Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 364 LEU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 482 LYS Chi-restraints excluded: chain L residue 501 ILE Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 526 VAL Chi-restraints excluded: chain L residue 612 GLU Chi-restraints excluded: chain L residue 684 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 8 optimal weight: 0.0070 chunk 148 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 278 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 49 GLN O 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.188523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.146837 restraints weight = 36273.477| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 3.63 r_work: 0.3827 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23048 Z= 0.115 Angle : 0.600 8.812 31266 Z= 0.302 Chirality : 0.046 0.239 3636 Planarity : 0.004 0.064 3983 Dihedral : 5.708 52.481 3299 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.08 % Allowed : 19.95 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.15), residues: 2916 helix: -0.26 (0.18), residues: 904 sheet: -1.35 (0.26), residues: 396 loop : -1.29 (0.14), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 601 TYR 0.016 0.001 TYR M 487 PHE 0.032 0.001 PHE O 378 TRP 0.015 0.001 TRP D 293 HIS 0.013 0.001 HIS N 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (23048) covalent geometry : angle 0.59963 / 0.30 (31266) hydrogen bonds : bond 0.03331 / 2.28 ( 698) hydrogen bonds : angle 5.35550 / 3.78 ( 1938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 250 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: D 52 SER cc_start: 0.8093 (t) cc_final: 0.7347 (m) REVERT: D 98 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7436 (tm-30) REVERT: D 133 GLN cc_start: 0.8314 (mt0) cc_final: 0.7817 (pp30) REVERT: D 135 LYS cc_start: 0.7010 (pptt) cc_final: 0.6519 (mmtp) REVERT: D 385 TRP cc_start: 0.6842 (m-90) cc_final: 0.6582 (m-90) REVERT: D 402 GLU cc_start: 0.8924 (tt0) cc_final: 0.8692 (tp30) REVERT: D 452 ARG cc_start: 0.6574 (ttp80) cc_final: 0.5755 (mtp85) REVERT: D 491 MET cc_start: 0.7659 (mmm) cc_final: 0.7105 (mmm) REVERT: D 517 MET cc_start: 0.6317 (ttm) cc_final: 0.5778 (ttm) REVERT: D 538 MET cc_start: 0.4796 (ttm) cc_final: 0.4578 (ttp) REVERT: M 256 ASP cc_start: 0.7676 (t0) cc_final: 0.7367 (m-30) REVERT: M 381 ASN cc_start: 0.7702 (t0) cc_final: 0.7329 (t0) REVERT: M 441 TRP cc_start: 0.7327 (m100) cc_final: 0.6920 (m100) REVERT: N 225 LYS cc_start: 0.7838 (pptt) cc_final: 0.6139 (tttt) REVERT: N 269 GLN cc_start: 0.4658 (tp-100) cc_final: 0.4299 (tm-30) REVERT: N 375 ARG cc_start: 0.3955 (OUTLIER) cc_final: 0.2766 (tpt90) REVERT: N 437 ASP cc_start: 0.6028 (m-30) cc_final: 0.5525 (p0) REVERT: N 458 LEU cc_start: 0.4903 (pp) cc_final: 0.4701 (pt) REVERT: N 576 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5759 (pp) REVERT: N 608 GLN cc_start: 0.4683 (tm-30) cc_final: 0.4096 (mm-40) REVERT: N 648 MET cc_start: 0.2373 (tpp) cc_final: 0.1891 (tpp) REVERT: O 24 ASN cc_start: 0.7702 (t0) cc_final: 0.7401 (m110) REVERT: O 66 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6734 (tt) REVERT: O 98 GLU cc_start: 0.7485 (tm-30) cc_final: 0.6804 (tm-30) REVERT: O 579 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6814 (p0) REVERT: O 600 TRP cc_start: 0.6557 (t60) cc_final: 0.5883 (t60) REVERT: O 651 GLU cc_start: 0.4679 (pp20) cc_final: 0.3528 (pt0) REVERT: O 686 GLN cc_start: 0.8335 (pt0) cc_final: 0.8033 (pt0) REVERT: L 79 LEU cc_start: 0.7234 (tt) cc_final: 0.6671 (mp) REVERT: L 80 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6098 (mt) REVERT: L 97 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.5585 (pm20) REVERT: L 297 TYR cc_start: 0.6897 (t80) cc_final: 0.6692 (t80) REVERT: L 361 ARG cc_start: 0.6463 (tpt170) cc_final: 0.5338 (mmm160) REVERT: L 419 MET cc_start: 0.8356 (mmp) cc_final: 0.8077 (mmp) REVERT: L 497 ARG cc_start: 0.8386 (tpt90) cc_final: 0.8095 (tpt90) REVERT: L 660 TYR cc_start: 0.6367 (m-10) cc_final: 0.6156 (m-10) outliers start: 50 outliers final: 38 residues processed: 293 average time/residue: 0.1610 time to fit residues: 73.3100 Evaluate side-chains 281 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 551 ILE Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 501 ILE Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 556 VAL Chi-restraints excluded: chain M residue 617 LEU Chi-restraints excluded: chain M residue 670 HIS Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 375 ARG Chi-restraints excluded: chain N residue 439 LEU Chi-restraints excluded: chain N residue 576 LEU Chi-restraints excluded: chain N residue 605 VAL Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 534 PHE Chi-restraints excluded: chain O residue 579 ASP Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 501 ILE Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 526 VAL Chi-restraints excluded: chain L residue 684 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 273 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 146 optimal weight: 20.0000 chunk 117 optimal weight: 40.0000 chunk 53 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 209 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.187038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.151485 restraints weight = 36372.733| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 3.75 r_work: 0.3800 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23048 Z= 0.139 Angle : 0.615 10.515 31266 Z= 0.309 Chirality : 0.046 0.220 3636 Planarity : 0.005 0.071 3983 Dihedral : 5.756 52.715 3299 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.50 % Allowed : 19.83 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.15), residues: 2916 helix: -0.24 (0.18), residues: 903 sheet: -1.29 (0.26), residues: 396 loop : -1.28 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 601 TYR 0.015 0.001 TYR L 60 PHE 0.029 0.001 PHE O 378 TRP 0.034 0.002 TRP D 293 HIS 0.013 0.001 HIS N 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (23048) covalent geometry : angle 0.61490 / 0.31 (31266) hydrogen bonds : bond 0.03538 / 2.42 ( 698) hydrogen bonds : angle 5.35324 / 3.78 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5201.20 seconds wall clock time: 90 minutes 3.16 seconds (5403.16 seconds total)