Starting phenix.real_space_refine on Thu May 22 09:05:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wj3_37577/05_2025/8wj3_37577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wj3_37577/05_2025/8wj3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wj3_37577/05_2025/8wj3_37577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wj3_37577/05_2025/8wj3_37577.map" model { file = "/net/cci-nas-00/data/ceres_data/8wj3_37577/05_2025/8wj3_37577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wj3_37577/05_2025/8wj3_37577.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG: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: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3} 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, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 6} 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, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP: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: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 5, 'HIS:plan': 4} 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: 13.78, per 1000 atoms: 0.61 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: 6.38 Conformation dependent library (CDL) restraints added in 2.9 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: 2.81 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: 7.66 Time building geometry restraints manager: 7.27 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=" C3' AGS M 701 " pdb=" C4' AGS M 701 " ideal model delta sigma weight residual 1.526 1.272 0.254 1.10e-02 8.26e+03 5.35e+02 bond pdb=" C3' AGS L 701 " pdb=" C4' AGS L 701 " ideal model delta sigma weight residual 1.526 1.274 0.252 1.10e-02 8.26e+03 5.25e+02 bond pdb=" C3' AGS O 701 " pdb=" C4' AGS O 701 " ideal model delta sigma weight residual 1.526 1.274 0.252 1.10e-02 8.26e+03 5.23e+02 bond pdb=" C1' AGS M 701 " pdb=" C2' AGS M 701 " ideal model delta sigma weight residual 1.530 1.275 0.255 1.30e-02 5.92e+03 3.86e+02 bond pdb=" C1' AGS L 701 " pdb=" C2' AGS L 701 " ideal model delta sigma weight residual 1.530 1.277 0.253 1.30e-02 5.92e+03 3.78e+02 ... (remaining 23043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 31016 2.67 - 5.34: 225 5.34 - 8.01: 13 8.01 - 10.68: 7 10.68 - 13.35: 5 Bond angle restraints: 31266 Sorted by residual: angle pdb=" N1 AGS M 701 " pdb=" C2 AGS M 701 " pdb=" N3 AGS M 701 " ideal model delta sigma weight residual 128.80 119.97 8.83 8.41e-01 1.41e+00 1.10e+02 angle pdb=" C5 AGS L 701 " pdb=" N7 AGS L 701 " pdb=" C8 AGS L 701 " ideal model delta sigma weight residual 103.67 108.14 -4.47 4.26e-01 5.51e+00 1.10e+02 angle pdb=" N1 AGS O 701 " pdb=" C2 AGS O 701 " pdb=" N3 AGS O 701 " ideal model delta sigma weight residual 128.80 120.04 8.76 8.41e-01 1.41e+00 1.08e+02 angle pdb=" N1 AGS L 701 " pdb=" C2 AGS L 701 " pdb=" N3 AGS L 701 " ideal model delta sigma weight residual 128.80 120.08 8.72 8.41e-01 1.41e+00 1.08e+02 angle pdb=" C5 AGS M 701 " pdb=" N7 AGS M 701 " pdb=" C8 AGS M 701 " ideal model delta sigma weight residual 103.67 108.03 -4.36 4.26e-01 5.51e+00 1.05e+02 ... (remaining 31261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.18: 13534 30.18 - 60.37: 321 60.37 - 90.55: 25 90.55 - 120.73: 0 120.73 - 150.91: 1 Dihedral angle restraints: 13881 sinusoidal: 5399 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 13878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2943 0.050 - 0.099: 482 0.099 - 0.149: 209 0.149 - 0.199: 4 0.199 - 0.248: 4 Chirality restraints: 3642 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 -2.67 -2.43 -0.25 2.00e-01 2.50e+01 1.54e+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 -2.67 -2.44 -0.24 2.00e-01 2.50e+01 1.41e+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 -2.67 -2.45 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3639 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 696 or resid 701 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 696 or resid 701 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 696 or resid 701 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 50.900 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.090 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 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 0.255 23048 Z= 0.474 Angle : 0.602 13.347 31266 Z= 0.394 Chirality : 0.044 0.248 3642 Planarity : 0.005 0.095 3983 Dihedral : 12.888 150.913 8433 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (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 TRP 0.055 0.002 TRP D 89 HIS 0.008 0.001 HIS L 162 PHE 0.019 0.001 PHE O 534 TYR 0.012 0.001 TYR O 130 ARG 0.012 0.000 ARG N 375 Details of bonding type rmsd hydrogen bonds : bond 0.27511 ( 698) hydrogen bonds : angle 9.72837 ( 1938) covalent geometry : bond 0.00626 (23048) covalent geometry : angle 0.60217 (31266) *********************** 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 : 2.414 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: 0.5599 (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: 0.5752 (m) REVERT: M 491 MET cc_start: 0.7313 (tpp) cc_final: 0.6676 (tpp) REVERT: N 375 ARG cc_start: 0.4555 (tmt170) cc_final: 0.3661 (tpt90) REVERT: N 486 LYS cc_start: 0.6654 (pptt) cc_final: 0.6281 (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: 0.6074 (pp) REVERT: O 98 GLU cc_start: 0.6623 (tm-30) cc_final: 0.5861 (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: 0.3507 time to fit residues: 193.5827 Evaluate side-chains 256 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 267 optimal weight: 0.9980 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 290 HIS D 388 ASN M 119 HIS M 201 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.187528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.150734 restraints weight = 35934.451| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 3.75 r_work: 0.3822 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 23048 Z= 0.206 Angle : 0.684 8.796 31266 Z= 0.357 Chirality : 0.050 0.184 3642 Planarity : 0.005 0.079 3983 Dihedral : 7.296 152.635 3245 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.46 % Allowed : 8.87 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.15), residues: 2916 helix: -0.60 (0.17), residues: 889 sheet: -1.63 (0.25), residues: 407 loop : -1.32 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 89 HIS 0.010 0.002 HIS L 162 PHE 0.021 0.002 PHE L 198 TYR 0.021 0.002 TYR O 13 ARG 0.005 0.001 ARG L 55 Details of bonding type rmsd hydrogen bonds : bond 0.06106 ( 698) hydrogen bonds : angle 6.58945 ( 1938) covalent geometry : bond 0.00499 (23048) covalent geometry : angle 0.68416 (31266) *********************** 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 322 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.6265 (pptt) cc_final: 0.5720 (mmtp) REVERT: D 263 LEU cc_start: 0.7782 (tp) cc_final: 0.7543 (pp) REVERT: D 437 ASP cc_start: 0.8176 (t0) cc_final: 0.7734 (t0) REVERT: D 492 MET cc_start: 0.6645 (ttm) cc_final: 0.6347 (ttm) REVERT: D 508 GLN cc_start: 0.5992 (OUTLIER) cc_final: 0.5350 (mp10) REVERT: D 538 MET cc_start: 0.5007 (ttm) cc_final: 0.4469 (mtp) REVERT: M 256 ASP cc_start: 0.7930 (t0) cc_final: 0.7669 (m-30) REVERT: M 381 ASN cc_start: 0.7590 (t0) cc_final: 0.7308 (t0) REVERT: M 491 MET cc_start: 0.7620 (tpp) cc_final: 0.7156 (tpp) REVERT: N 223 GLU cc_start: 0.3398 (tp30) cc_final: 0.1493 (tt0) REVERT: N 375 ARG cc_start: 0.4402 (tmt170) cc_final: 0.3195 (tpt90) REVERT: N 478 ARG cc_start: 0.7979 (mtm180) cc_final: 0.7129 (mtp180) REVERT: N 492 MET cc_start: 0.7898 (tpt) cc_final: 0.7275 (ttt) REVERT: N 576 LEU cc_start: 0.6687 (mp) cc_final: 0.6027 (pp) REVERT: N 651 GLU cc_start: 0.7251 (tt0) cc_final: 0.5901 (pm20) REVERT: O 19 ASP cc_start: 0.7660 (t0) cc_final: 0.7374 (t0) REVERT: O 98 GLU cc_start: 0.7485 (tm-30) cc_final: 0.6706 (tm-30) REVERT: O 268 ARG cc_start: 0.7656 (ptp90) cc_final: 0.7018 (ptp90) REVERT: O 362 LYS cc_start: 0.8232 (tmmt) cc_final: 0.7954 (ttpt) REVERT: O 480 ILE cc_start: 0.8059 (mt) cc_final: 0.7845 (mt) REVERT: O 600 TRP cc_start: 0.6460 (t60) cc_final: 0.5453 (t60) REVERT: L 497 ARG cc_start: 0.8533 (tpt90) cc_final: 0.8200 (tpt90) outliers start: 35 outliers final: 23 residues processed: 313 average time/residue: 0.3829 time to fit residues: 181.5587 Evaluate side-chains 267 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 2.594 ------------------------------------------------------------------------------- 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 290 HIS Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 188 SER 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 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 408 GLU Chi-restraints excluded: chain O residue 469 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 530 VAL 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 84 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 217 optimal weight: 0.2980 chunk 91 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 230 optimal weight: 30.0000 chunk 164 optimal weight: 0.7980 chunk 262 optimal weight: 5.9990 chunk 184 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN D 62 ASN N 49 GLN N 381 ASN O 670 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.191419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.154565 restraints weight = 35596.628| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 3.57 r_work: 0.3881 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23048 Z= 0.116 Angle : 0.575 11.667 31266 Z= 0.295 Chirality : 0.046 0.225 3642 Planarity : 0.004 0.076 3983 Dihedral : 7.055 151.889 3245 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.37 % Allowed : 12.49 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.15), residues: 2916 helix: -0.32 (0.18), residues: 892 sheet: -1.39 (0.24), residues: 423 loop : -1.13 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 89 HIS 0.028 0.001 HIS D 290 PHE 0.016 0.001 PHE D 243 TYR 0.026 0.001 TYR O 130 ARG 0.004 0.000 ARG N 601 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 698) hydrogen bonds : angle 5.90254 ( 1938) covalent geometry : bond 0.00262 (23048) covalent geometry : angle 0.57522 (31266) *********************** 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 316 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.6352 (pptt) cc_final: 0.5717 (mmtp) REVERT: D 452 ARG cc_start: 0.6368 (ttp80) cc_final: 0.5194 (ttp80) REVERT: M 163 SER cc_start: 0.7710 (m) cc_final: 0.7298 (t) REVERT: M 256 ASP cc_start: 0.7980 (t0) cc_final: 0.7716 (m-30) REVERT: M 268 ARG cc_start: 0.6776 (tpm170) cc_final: 0.6556 (tpm170) REVERT: M 381 ASN cc_start: 0.7584 (t0) cc_final: 0.7251 (t0) REVERT: M 491 MET cc_start: 0.7439 (tpp) cc_final: 0.7074 (tpp) REVERT: N 297 TYR cc_start: 0.1972 (m-80) cc_final: 0.1698 (m-80) REVERT: N 437 ASP cc_start: 0.5679 (m-30) cc_final: 0.4941 (p0) REVERT: N 458 LEU cc_start: 0.5233 (pp) cc_final: 0.4976 (pt) REVERT: N 492 MET cc_start: 0.7777 (tpt) cc_final: 0.7280 (ttt) REVERT: N 576 LEU cc_start: 0.6650 (mp) cc_final: 0.6016 (pp) REVERT: N 651 GLU cc_start: 0.7330 (tt0) cc_final: 0.5754 (pm20) REVERT: N 672 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8659 (pm20) REVERT: O 98 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6606 (tm-30) REVERT: O 362 LYS cc_start: 0.8325 (tmmt) cc_final: 0.7974 (ttpp) REVERT: O 600 TRP cc_start: 0.6621 (t60) cc_final: 0.6016 (t60) REVERT: L 69 GLN cc_start: 0.8248 (mt0) cc_final: 0.7734 (mp-120) REVERT: L 378 PHE cc_start: 0.7916 (p90) cc_final: 0.7710 (p90) REVERT: L 497 ARG cc_start: 0.8341 (tpt90) cc_final: 0.8093 (tpt90) outliers start: 33 outliers final: 16 residues processed: 309 average time/residue: 0.3488 time to fit residues: 166.5357 Evaluate side-chains 257 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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 214 VAL 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 N residue 672 GLU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 614 ILE 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 98 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 292 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 444 ASN N 49 GLN N 381 ASN ** O 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.182627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.143701 restraints weight = 36685.647| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 3.56 r_work: 0.3775 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 23048 Z= 0.296 Angle : 0.759 11.326 31266 Z= 0.390 Chirality : 0.052 0.249 3642 Planarity : 0.006 0.078 3983 Dihedral : 7.648 152.118 3245 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.29 % Allowed : 15.20 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 2916 helix: -0.75 (0.17), residues: 889 sheet: -1.62 (0.25), residues: 406 loop : -1.50 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP N 600 HIS 0.014 0.002 HIS L 162 PHE 0.025 0.003 PHE L 440 TYR 0.030 0.003 TYR O 215 ARG 0.011 0.001 ARG L 485 Details of bonding type rmsd hydrogen bonds : bond 0.05297 ( 698) hydrogen bonds : angle 6.12006 ( 1938) covalent geometry : bond 0.00726 (23048) covalent geometry : angle 0.75947 (31266) *********************** 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 329 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 250 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8128 (t) cc_final: 0.7357 (m) REVERT: D 419 MET cc_start: 0.7287 (mtp) cc_final: 0.6944 (mtp) REVERT: D 508 GLN cc_start: 0.6076 (OUTLIER) cc_final: 0.5441 (mp10) REVERT: M 90 ILE cc_start: 0.2638 (OUTLIER) cc_final: 0.2377 (pt) REVERT: M 381 ASN cc_start: 0.7826 (t0) cc_final: 0.7474 (t0) REVERT: M 447 GLU cc_start: 0.6339 (pp20) cc_final: 0.5214 (pp20) REVERT: M 480 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7424 (mp) REVERT: M 491 MET cc_start: 0.7494 (tpp) cc_final: 0.7011 (tpp) REVERT: N 215 TYR cc_start: 0.5569 (m-80) cc_final: 0.5319 (m-80) REVERT: N 225 LYS cc_start: 0.7951 (pptt) cc_final: 0.7564 (pptt) REVERT: N 269 GLN cc_start: 0.4959 (tp-100) cc_final: 0.4540 (tm-30) REVERT: N 297 TYR cc_start: 0.2172 (m-80) cc_final: 0.1750 (m-80) REVERT: N 492 MET cc_start: 0.7762 (tpt) cc_final: 0.7262 (ttt) REVERT: N 560 MET cc_start: 0.5029 (pmm) cc_final: 0.3785 (mtm) REVERT: N 576 LEU cc_start: 0.6779 (mp) cc_final: 0.5990 (pp) REVERT: N 651 GLU cc_start: 0.7313 (tt0) cc_final: 0.5665 (pm20) REVERT: O 98 GLU cc_start: 0.7729 (tm-30) cc_final: 0.6952 (tm-30) REVERT: O 215 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.7113 (m-10) REVERT: O 497 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7036 (tpt170) REVERT: O 560 MET cc_start: 0.6429 (mmt) cc_final: 0.6037 (mmt) REVERT: O 579 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6654 (p0) REVERT: O 600 TRP cc_start: 0.6462 (t60) cc_final: 0.5694 (t60) outliers start: 79 outliers final: 46 residues processed: 312 average time/residue: 0.3558 time to fit residues: 171.6137 Evaluate side-chains 276 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 2.685 ------------------------------------------------------------------------------- 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 126 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 184 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 432 ILE Chi-restraints excluded: chain M residue 480 ILE 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 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 564 ILE Chi-restraints excluded: chain N residue 670 HIS 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 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 527 LEU 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 614 ILE Chi-restraints excluded: chain L residue 684 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 260 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 263 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 271 optimal weight: 0.9980 chunk 2 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 20 optimal weight: 0.0030 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 49 GLN ** N 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 445 GLN O 670 HIS L 290 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.187313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.150219 restraints weight = 35922.815| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.77 r_work: 0.3821 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23048 Z= 0.131 Angle : 0.596 9.999 31266 Z= 0.305 Chirality : 0.047 0.207 3642 Planarity : 0.004 0.078 3983 Dihedral : 7.189 153.433 3245 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.83 % Allowed : 16.99 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.15), residues: 2916 helix: -0.52 (0.17), residues: 905 sheet: -1.39 (0.25), residues: 407 loop : -1.32 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP N 600 HIS 0.010 0.001 HIS N 670 PHE 0.025 0.001 PHE O 378 TYR 0.012 0.001 TYR M 436 ARG 0.003 0.000 ARG M 443 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 698) hydrogen bonds : angle 5.69664 ( 1938) covalent geometry : bond 0.00311 (23048) covalent geometry : angle 0.59625 (31266) *********************** 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 326 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 258 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8345 (t) cc_final: 0.7549 (m) REVERT: D 98 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7346 (tm-30) REVERT: D 133 GLN cc_start: 0.8254 (mt0) cc_final: 0.7724 (pp30) REVERT: D 135 LYS cc_start: 0.6599 (pptt) cc_final: 0.6070 (mmtp) REVERT: D 508 GLN cc_start: 0.6045 (OUTLIER) cc_final: 0.5508 (mp10) REVERT: M 256 ASP cc_start: 0.7972 (t0) cc_final: 0.7661 (m-30) REVERT: M 381 ASN cc_start: 0.7716 (t0) cc_final: 0.7326 (t0) REVERT: M 447 GLU cc_start: 0.6473 (pp20) cc_final: 0.5590 (pp20) REVERT: M 491 MET cc_start: 0.7365 (tpp) cc_final: 0.6823 (tpp) REVERT: N 269 GLN cc_start: 0.4979 (tp-100) cc_final: 0.4512 (tm-30) REVERT: N 297 TYR cc_start: 0.2561 (m-80) cc_final: 0.2154 (m-80) REVERT: N 375 ARG cc_start: 0.4351 (OUTLIER) cc_final: 0.3006 (tpt90) REVERT: N 419 MET cc_start: 0.2889 (mmt) cc_final: 0.2190 (mmt) REVERT: N 437 ASP cc_start: 0.5743 (m-30) cc_final: 0.5124 (p0) REVERT: N 492 MET cc_start: 0.7678 (tpt) cc_final: 0.7345 (ttt) REVERT: N 560 MET cc_start: 0.4768 (pmm) cc_final: 0.4043 (mtt) REVERT: N 576 LEU cc_start: 0.6802 (mp) cc_final: 0.6010 (pp) REVERT: N 651 GLU cc_start: 0.7341 (tt0) cc_final: 0.5631 (pm20) REVERT: O 98 GLU cc_start: 0.7544 (tm-30) cc_final: 0.6839 (tm-30) REVERT: O 497 ARG cc_start: 0.7241 (ttm-80) cc_final: 0.6841 (ttm-80) REVERT: O 579 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6564 (p0) REVERT: O 600 TRP cc_start: 0.6586 (t60) cc_final: 0.5874 (t60) REVERT: O 651 GLU cc_start: 0.4949 (pp20) cc_final: 0.3604 (pt0) REVERT: L 66 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.6740 (mm) REVERT: L 378 PHE cc_start: 0.7993 (p90) cc_final: 0.7743 (p90) outliers start: 68 outliers final: 34 residues processed: 314 average time/residue: 0.3476 time to fit residues: 168.8737 Evaluate side-chains 273 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 508 GLN 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 235 CYS Chi-restraints excluded: chain M residue 278 SER Chi-restraints excluded: chain M residue 432 ILE Chi-restraints excluded: chain M residue 438 SER 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 670 HIS Chi-restraints excluded: chain N residue 121 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 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 469 SER 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 218 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 684 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 100 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 275 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 283 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 175 optimal weight: 0.4980 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 49 GLN N 656 HIS N 679 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.185340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.148277 restraints weight = 36158.162| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 3.75 r_work: 0.3796 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23048 Z= 0.174 Angle : 0.625 8.869 31266 Z= 0.318 Chirality : 0.048 0.183 3642 Planarity : 0.005 0.074 3983 Dihedral : 7.239 151.444 3245 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.25 % Allowed : 17.49 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.15), residues: 2916 helix: -0.49 (0.17), residues: 901 sheet: -1.42 (0.25), residues: 407 loop : -1.33 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP N 600 HIS 0.011 0.001 HIS L 162 PHE 0.017 0.002 PHE O 378 TYR 0.018 0.002 TYR O 215 ARG 0.007 0.000 ARG N 601 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 698) hydrogen bonds : angle 5.63923 ( 1938) covalent geometry : bond 0.00424 (23048) covalent geometry : angle 0.62532 (31266) *********************** 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 323 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 245 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8342 (t) cc_final: 0.7539 (m) REVERT: D 98 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7365 (tm-30) REVERT: D 133 GLN cc_start: 0.8307 (mt0) cc_final: 0.7917 (pp30) REVERT: D 508 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5564 (mp10) REVERT: M 162 HIS cc_start: 0.7418 (OUTLIER) cc_final: 0.6889 (m90) REVERT: M 381 ASN cc_start: 0.7864 (t0) cc_final: 0.7446 (t0) REVERT: M 427 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8044 (mm) REVERT: M 447 GLU cc_start: 0.6246 (pp20) cc_final: 0.5338 (pp20) REVERT: N 246 LEU cc_start: 0.4320 (mm) cc_final: 0.4073 (mt) REVERT: N 269 GLN cc_start: 0.5255 (tp-100) cc_final: 0.4716 (tm-30) REVERT: N 297 TYR cc_start: 0.2571 (m-80) cc_final: 0.2316 (m-80) REVERT: N 375 ARG cc_start: 0.4301 (OUTLIER) cc_final: 0.2858 (tpt90) REVERT: N 419 MET cc_start: 0.3026 (mmt) cc_final: 0.2310 (mmt) REVERT: N 437 ASP cc_start: 0.5796 (m-30) cc_final: 0.5199 (p0) REVERT: N 492 MET cc_start: 0.7733 (tpt) cc_final: 0.7347 (ttt) REVERT: N 560 MET cc_start: 0.4522 (pmm) cc_final: 0.3776 (mtt) REVERT: N 576 LEU cc_start: 0.6744 (mp) cc_final: 0.5957 (pp) REVERT: N 651 GLU cc_start: 0.7331 (tt0) cc_final: 0.5825 (pm20) REVERT: O 98 GLU cc_start: 0.7648 (tm-30) cc_final: 0.6893 (tm-30) REVERT: O 126 LEU cc_start: 0.8221 (tt) cc_final: 0.7884 (pp) REVERT: O 338 ILE cc_start: 0.7795 (mp) cc_final: 0.7288 (tp) REVERT: O 497 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.6946 (ttm-80) REVERT: O 579 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6658 (p0) REVERT: O 600 TRP cc_start: 0.6428 (t60) cc_final: 0.5745 (t60) REVERT: O 651 GLU cc_start: 0.4945 (pp20) cc_final: 0.3643 (pt0) REVERT: L 69 GLN cc_start: 0.8348 (mt0) cc_final: 0.7958 (mp-120) REVERT: L 80 LEU cc_start: 0.5594 (OUTLIER) cc_final: 0.5052 (tt) REVERT: L 247 GLU cc_start: 0.7920 (pm20) cc_final: 0.7677 (mp0) REVERT: L 378 PHE cc_start: 0.7961 (p90) cc_final: 0.7736 (p90) REVERT: L 545 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7430 (ttm110) outliers start: 78 outliers final: 50 residues processed: 312 average time/residue: 0.3287 time to fit residues: 160.6302 Evaluate side-chains 278 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 221 time to evaluate : 2.438 ------------------------------------------------------------------------------- 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 292 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 508 GLN 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 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 241 VAL Chi-restraints excluded: chain M residue 278 SER Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain M residue 427 LEU 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 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 564 ILE Chi-restraints excluded: chain N residue 605 VAL 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 408 GLU 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 517 MET 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 457 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 83 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 279 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 241 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.187643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.150955 restraints weight = 36080.755| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 3.81 r_work: 0.3818 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23048 Z= 0.124 Angle : 0.589 8.517 31266 Z= 0.298 Chirality : 0.046 0.179 3642 Planarity : 0.004 0.073 3983 Dihedral : 6.990 150.019 3245 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.79 % Allowed : 18.58 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 2916 helix: -0.26 (0.18), residues: 899 sheet: -1.36 (0.25), residues: 409 loop : -1.21 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 600 HIS 0.012 0.001 HIS N 670 PHE 0.019 0.001 PHE O 378 TYR 0.015 0.001 TYR O 130 ARG 0.008 0.000 ARG N 601 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 698) hydrogen bonds : angle 5.43372 ( 1938) covalent geometry : bond 0.00295 (23048) covalent geometry : angle 0.58907 (31266) *********************** 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 313 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 246 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8362 (t) cc_final: 0.7594 (m) REVERT: D 98 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7310 (tm-30) REVERT: D 133 GLN cc_start: 0.8201 (mt0) cc_final: 0.7762 (pp30) REVERT: D 135 LYS cc_start: 0.6687 (pptt) cc_final: 0.6252 (mmtp) REVERT: D 452 ARG cc_start: 0.6604 (ttp80) cc_final: 0.5778 (mtp85) REVERT: D 491 MET cc_start: 0.8202 (mmm) cc_final: 0.7273 (mmm) REVERT: D 538 MET cc_start: 0.4732 (ttm) cc_final: 0.4427 (ttm) REVERT: M 263 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6994 (mt) REVERT: M 381 ASN cc_start: 0.7796 (t0) cc_final: 0.7387 (t0) REVERT: M 427 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7987 (mm) REVERT: M 467 LYS cc_start: 0.6704 (mmtt) cc_final: 0.6251 (mmtt) REVERT: M 491 MET cc_start: 0.7432 (tpp) cc_final: 0.6909 (tpp) REVERT: N 49 GLN cc_start: 0.3010 (OUTLIER) cc_final: 0.2483 (pm20) REVERT: N 375 ARG cc_start: 0.4262 (OUTLIER) cc_final: 0.2922 (tpt90) REVERT: N 419 MET cc_start: 0.3554 (mmt) cc_final: 0.2781 (mmt) REVERT: N 437 ASP cc_start: 0.5849 (m-30) cc_final: 0.5285 (p0) REVERT: N 492 MET cc_start: 0.7802 (tpt) cc_final: 0.7499 (ttt) REVERT: N 576 LEU cc_start: 0.6775 (mp) cc_final: 0.5933 (pp) REVERT: N 651 GLU cc_start: 0.7580 (tt0) cc_final: 0.5886 (pm20) REVERT: O 126 LEU cc_start: 0.8143 (tt) cc_final: 0.7861 (pp) REVERT: O 338 ILE cc_start: 0.7712 (mp) cc_final: 0.7203 (tp) REVERT: O 497 ARG cc_start: 0.7172 (ttm-80) cc_final: 0.6783 (ttm-80) REVERT: O 579 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6566 (p0) REVERT: O 600 TRP cc_start: 0.6597 (t60) cc_final: 0.5925 (t60) REVERT: O 651 GLU cc_start: 0.4905 (pp20) cc_final: 0.3614 (pt0) REVERT: L 66 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6611 (mm) REVERT: L 69 GLN cc_start: 0.8264 (mt0) cc_final: 0.7945 (mp-120) REVERT: L 79 LEU cc_start: 0.7223 (tt) cc_final: 0.6580 (mp) REVERT: L 80 LEU cc_start: 0.5392 (OUTLIER) cc_final: 0.4872 (tt) REVERT: L 247 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: L 361 ARG cc_start: 0.6338 (tpt170) cc_final: 0.4978 (mmm160) REVERT: L 367 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6623 (tp) REVERT: L 545 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7383 (ttm110) outliers start: 67 outliers final: 41 residues processed: 303 average time/residue: 0.3432 time to fit residues: 161.9098 Evaluate side-chains 279 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 2.508 ------------------------------------------------------------------------------- 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 156 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 432 ILE 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 670 HIS Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 49 GLN 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 494 VAL 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 155 ILE 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 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 218 THR Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 247 GLU Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 360 ILE Chi-restraints excluded: chain L residue 367 LEU Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 545 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 270 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 chunk 220 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 chunk 172 optimal weight: 0.3980 chunk 189 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.189925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.147021 restraints weight = 35898.962| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 3.54 r_work: 0.3865 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23048 Z= 0.107 Angle : 0.575 11.742 31266 Z= 0.292 Chirality : 0.045 0.223 3642 Planarity : 0.004 0.071 3983 Dihedral : 6.754 146.861 3245 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.42 % Allowed : 18.95 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 2916 helix: -0.11 (0.18), residues: 908 sheet: -1.28 (0.26), residues: 399 loop : -1.08 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 600 HIS 0.011 0.001 HIS N 670 PHE 0.024 0.001 PHE L 378 TYR 0.019 0.001 TYR M 487 ARG 0.004 0.000 ARG D 375 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 698) hydrogen bonds : angle 5.25392 ( 1938) covalent geometry : bond 0.00242 (23048) covalent geometry : angle 0.57546 (31266) *********************** 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 310 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 98 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7242 (tm-30) REVERT: D 133 GLN cc_start: 0.8166 (mt0) cc_final: 0.7704 (pp30) REVERT: D 135 LYS cc_start: 0.6769 (pptt) cc_final: 0.6298 (mmtp) REVERT: D 402 GLU cc_start: 0.8904 (tt0) cc_final: 0.8692 (tp30) REVERT: D 452 ARG cc_start: 0.6434 (ttp80) cc_final: 0.5610 (mtp85) REVERT: D 491 MET cc_start: 0.8024 (mmm) cc_final: 0.7196 (mmm) REVERT: D 538 MET cc_start: 0.4799 (ttm) cc_final: 0.4573 (ttm) REVERT: M 263 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6970 (mt) REVERT: M 381 ASN cc_start: 0.7730 (t0) cc_final: 0.7345 (t0) REVERT: M 427 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7791 (mm) REVERT: M 467 LYS cc_start: 0.6894 (mmtt) cc_final: 0.6583 (mmtt) REVERT: N 375 ARG cc_start: 0.4337 (OUTLIER) cc_final: 0.3038 (tpt90) REVERT: N 419 MET cc_start: 0.3195 (mmt) cc_final: 0.2508 (mmt) REVERT: N 437 ASP cc_start: 0.6231 (m-30) cc_final: 0.5649 (p0) REVERT: N 492 MET cc_start: 0.7647 (tpt) cc_final: 0.7356 (ttt) REVERT: N 576 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.5809 (pp) REVERT: N 648 MET cc_start: 0.2055 (tpp) cc_final: 0.1735 (tpp) REVERT: N 651 GLU cc_start: 0.7439 (tt0) cc_final: 0.6931 (tt0) REVERT: O 24 ASN cc_start: 0.7688 (t0) cc_final: 0.7409 (m110) REVERT: O 126 LEU cc_start: 0.8230 (tt) cc_final: 0.7982 (pp) REVERT: O 497 ARG cc_start: 0.7043 (ttm-80) cc_final: 0.6599 (ttm-80) REVERT: O 579 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6768 (p0) REVERT: O 600 TRP cc_start: 0.6595 (t60) cc_final: 0.5957 (t60) REVERT: O 651 GLU cc_start: 0.4797 (pp20) cc_final: 0.3574 (pt0) REVERT: L 66 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6509 (mm) REVERT: L 69 GLN cc_start: 0.8154 (mt0) cc_final: 0.7831 (mp-120) REVERT: L 79 LEU cc_start: 0.7136 (tt) cc_final: 0.6600 (mp) REVERT: L 80 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5199 (tt) REVERT: L 247 GLU cc_start: 0.7862 (pm20) cc_final: 0.7624 (mp0) REVERT: L 297 TYR cc_start: 0.6842 (t80) cc_final: 0.6584 (t80) REVERT: L 361 ARG cc_start: 0.6058 (tpt170) cc_final: 0.4858 (mmm160) REVERT: L 545 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7157 (ttm110) outliers start: 58 outliers final: 38 residues processed: 301 average time/residue: 0.3292 time to fit residues: 154.3568 Evaluate side-chains 278 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 75 VAL Chi-restraints excluded: chain M residue 156 ASP Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 188 SER Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain M residue 427 LEU 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 149 ILE Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 296 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 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 432 ILE Chi-restraints excluded: chain O residue 469 SER Chi-restraints excluded: chain O residue 506 LEU 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 218 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 360 ILE Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 545 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 112 optimal weight: 30.0000 chunk 133 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 77 optimal weight: 0.0570 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 35 optimal weight: 0.0770 chunk 4 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.185367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.148525 restraints weight = 36216.225| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.65 r_work: 0.3792 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23048 Z= 0.181 Angle : 0.647 11.276 31266 Z= 0.326 Chirality : 0.048 0.366 3642 Planarity : 0.005 0.069 3983 Dihedral : 6.994 145.680 3245 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.71 % Allowed : 18.87 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.15), residues: 2916 helix: -0.29 (0.18), residues: 910 sheet: -1.30 (0.25), residues: 408 loop : -1.16 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 600 HIS 0.013 0.001 HIS L 162 PHE 0.019 0.002 PHE L 440 TYR 0.012 0.002 TYR O 130 ARG 0.004 0.000 ARG L 485 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 698) hydrogen bonds : angle 5.39033 ( 1938) covalent geometry : bond 0.00443 (23048) covalent geometry : angle 0.64657 (31266) *********************** 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 301 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8412 (t) cc_final: 0.7643 (m) REVERT: D 133 GLN cc_start: 0.8243 (mt0) cc_final: 0.7763 (pp30) REVERT: D 135 LYS cc_start: 0.6656 (pptt) cc_final: 0.6235 (mmtp) REVERT: D 452 ARG cc_start: 0.6640 (ttp80) cc_final: 0.5731 (mtp85) REVERT: D 491 MET cc_start: 0.7984 (mmm) cc_final: 0.7199 (mmm) REVERT: D 517 MET cc_start: 0.6339 (ttm) cc_final: 0.5821 (ttm) REVERT: D 538 MET cc_start: 0.4575 (ttm) cc_final: 0.4350 (ttm) REVERT: M 263 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7014 (mt) REVERT: M 271 TYR cc_start: 0.8411 (m-80) cc_final: 0.8207 (m-80) REVERT: M 381 ASN cc_start: 0.7787 (t0) cc_final: 0.7404 (t0) REVERT: M 427 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8052 (mm) REVERT: M 447 GLU cc_start: 0.6177 (pp20) cc_final: 0.5195 (pp20) REVERT: M 467 LYS cc_start: 0.6912 (mmtt) cc_final: 0.6492 (mmtt) REVERT: M 491 MET cc_start: 0.7446 (tpp) cc_final: 0.6927 (tpp) REVERT: N 375 ARG cc_start: 0.4018 (OUTLIER) cc_final: 0.2487 (tpt90) REVERT: N 419 MET cc_start: 0.3565 (mmt) cc_final: 0.2710 (mmt) REVERT: N 437 ASP cc_start: 0.5935 (m-30) cc_final: 0.5373 (p0) REVERT: N 492 MET cc_start: 0.7688 (tpt) cc_final: 0.7341 (ttt) REVERT: N 560 MET cc_start: 0.5188 (pmm) cc_final: 0.3568 (mtm) REVERT: N 576 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.5929 (pp) REVERT: N 648 MET cc_start: 0.2124 (tpp) cc_final: 0.1832 (tpp) REVERT: O 98 GLU cc_start: 0.7593 (tm-30) cc_final: 0.6838 (tm-30) REVERT: O 497 ARG cc_start: 0.7330 (ttm-80) cc_final: 0.6906 (ttm-80) REVERT: O 579 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6678 (p0) REVERT: O 600 TRP cc_start: 0.6534 (t60) cc_final: 0.5894 (t60) REVERT: O 651 GLU cc_start: 0.4907 (pp20) cc_final: 0.3680 (pt0) REVERT: L 69 GLN cc_start: 0.8337 (mt0) cc_final: 0.8047 (mp-120) REVERT: L 80 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5390 (tt) REVERT: L 247 GLU cc_start: 0.7883 (pm20) cc_final: 0.7626 (mp0) REVERT: L 361 ARG cc_start: 0.6317 (tpt170) cc_final: 0.5086 (mmm160) REVERT: L 482 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7336 (mttt) REVERT: L 545 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7479 (ttm110) outliers start: 65 outliers final: 53 residues processed: 290 average time/residue: 0.3405 time to fit residues: 153.6776 Evaluate side-chains 294 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 233 time to evaluate : 2.751 ------------------------------------------------------------------------------- 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 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 156 ASP Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 188 SER Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 501 ILE 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 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 494 VAL 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 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 249 SER Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 408 GLU 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 517 MET 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 218 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 457 VAL Chi-restraints excluded: chain L residue 482 LYS Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 545 ARG Chi-restraints excluded: chain L residue 612 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 76 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 176 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 255 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 183 optimal weight: 0.0470 chunk 250 optimal weight: 0.0770 chunk 56 optimal weight: 30.0000 overall best weight: 1.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.187091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.145687 restraints weight = 35990.911| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 3.44 r_work: 0.3837 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23048 Z= 0.130 Angle : 0.607 11.144 31266 Z= 0.306 Chirality : 0.047 0.327 3642 Planarity : 0.004 0.070 3983 Dihedral : 6.841 143.955 3245 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.50 % Allowed : 19.24 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 2916 helix: -0.20 (0.18), residues: 913 sheet: -1.26 (0.26), residues: 398 loop : -1.14 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 600 HIS 0.013 0.001 HIS N 670 PHE 0.021 0.001 PHE L 378 TYR 0.013 0.001 TYR M 487 ARG 0.004 0.000 ARG D 375 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 698) hydrogen bonds : angle 5.30432 ( 1938) covalent geometry : bond 0.00313 (23048) covalent geometry : angle 0.60744 (31266) ********************** 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 296 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8309 (t) cc_final: 0.7513 (m) REVERT: D 98 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7542 (tm-30) REVERT: D 133 GLN cc_start: 0.8242 (mt0) cc_final: 0.7778 (pp30) REVERT: D 135 LYS cc_start: 0.6695 (pptt) cc_final: 0.6234 (mmtp) REVERT: D 385 TRP cc_start: 0.6945 (m-90) cc_final: 0.6665 (m-90) REVERT: D 402 GLU cc_start: 0.8924 (tt0) cc_final: 0.8716 (tp30) REVERT: D 452 ARG cc_start: 0.6562 (ttp80) cc_final: 0.5731 (mtp85) REVERT: D 517 MET cc_start: 0.6231 (ttm) cc_final: 0.5723 (ttm) REVERT: D 538 MET cc_start: 0.4699 (ttm) cc_final: 0.4468 (ttp) REVERT: M 263 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7010 (mt) REVERT: M 271 TYR cc_start: 0.8356 (m-80) cc_final: 0.8147 (m-80) REVERT: M 381 ASN cc_start: 0.7858 (t0) cc_final: 0.7465 (t0) REVERT: M 427 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7960 (mm) REVERT: M 447 GLU cc_start: 0.6069 (pp20) cc_final: 0.5193 (pp20) REVERT: M 467 LYS cc_start: 0.6934 (mmtt) cc_final: 0.6464 (mmtt) REVERT: M 491 MET cc_start: 0.7364 (tpp) cc_final: 0.6866 (tpp) REVERT: M 543 THR cc_start: 0.6610 (m) cc_final: 0.6173 (t) REVERT: N 375 ARG cc_start: 0.3919 (OUTLIER) cc_final: 0.2575 (tpt90) REVERT: N 419 MET cc_start: 0.3509 (mmt) cc_final: 0.2683 (mmt) REVERT: N 437 ASP cc_start: 0.6085 (m-30) cc_final: 0.5582 (p0) REVERT: N 560 MET cc_start: 0.5209 (pmm) cc_final: 0.3560 (mtm) REVERT: N 576 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.5809 (pp) REVERT: N 648 MET cc_start: 0.1955 (tpp) cc_final: 0.1663 (tpp) REVERT: O 24 ASN cc_start: 0.7762 (t0) cc_final: 0.7486 (m110) REVERT: O 98 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6827 (tm-30) REVERT: O 126 LEU cc_start: 0.7903 (pp) cc_final: 0.7362 (tt) REVERT: O 497 ARG cc_start: 0.7154 (ttm-80) cc_final: 0.6736 (ttm-80) REVERT: O 579 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6771 (p0) REVERT: O 600 TRP cc_start: 0.6621 (t60) cc_final: 0.5968 (t60) REVERT: O 651 GLU cc_start: 0.4785 (pp20) cc_final: 0.3583 (pt0) REVERT: L 66 ILE cc_start: 0.7185 (OUTLIER) cc_final: 0.6547 (mm) REVERT: L 69 GLN cc_start: 0.8283 (mt0) cc_final: 0.7958 (mp-120) REVERT: L 79 LEU cc_start: 0.7213 (tt) cc_final: 0.6674 (mp) REVERT: L 80 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5468 (tt) REVERT: L 247 GLU cc_start: 0.7891 (pm20) cc_final: 0.7646 (mp0) REVERT: L 297 TYR cc_start: 0.6873 (t80) cc_final: 0.6625 (t80) REVERT: L 361 ARG cc_start: 0.6133 (tpt170) cc_final: 0.4959 (mmm160) REVERT: L 482 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7256 (mttt) REVERT: L 545 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7364 (ttm110) outliers start: 60 outliers final: 48 residues processed: 290 average time/residue: 0.3286 time to fit residues: 148.1360 Evaluate side-chains 290 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 233 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 156 ASP 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 263 LEU Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain M residue 427 LEU 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 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 494 VAL 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 292 LEU Chi-restraints excluded: chain O residue 387 VAL 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 218 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 360 ILE Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 482 LYS Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 545 ARG Chi-restraints excluded: chain L residue 612 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 170 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 79 optimal weight: 0.0170 chunk 204 optimal weight: 4.9990 chunk 220 optimal weight: 0.0070 chunk 175 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 260 optimal weight: 0.0570 chunk 194 optimal weight: 8.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 445 GLN ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.191093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.150227 restraints weight = 35962.813| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.66 r_work: 0.3882 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23048 Z= 0.102 Angle : 0.574 10.392 31266 Z= 0.289 Chirality : 0.045 0.320 3642 Planarity : 0.004 0.066 3983 Dihedral : 6.494 139.592 3245 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.00 % Allowed : 19.66 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 2916 helix: 0.00 (0.18), residues: 909 sheet: -1.03 (0.26), residues: 397 loop : -1.02 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 404 HIS 0.014 0.001 HIS N 670 PHE 0.020 0.001 PHE O 378 TYR 0.012 0.001 TYR M 487 ARG 0.005 0.000 ARG D 452 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 698) hydrogen bonds : angle 5.09710 ( 1938) covalent geometry : bond 0.00233 (23048) covalent geometry : angle 0.57381 (31266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11133.54 seconds wall clock time: 193 minutes 26.36 seconds (11606.36 seconds total)