Starting phenix.real_space_refine on Thu Jun 19 16:06:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wj3_37577/06_2025/8wj3_37577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wj3_37577/06_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_37577/06_2025/8wj3_37577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wj3_37577/06_2025/8wj3_37577.map" model { file = "/net/cci-nas-00/data/ceres_data/8wj3_37577/06_2025/8wj3_37577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wj3_37577/06_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-5710/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: 13.58, per 1000 atoms: 0.60 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: 5.54 Conformation dependent library (CDL) restraints added in 3.0 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: 3.06 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: 8.12 Time building geometry restraints manager: 6.55 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: 1.270 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: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 51.930 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.100 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.810 ------------------------------------------------------------------------------- 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 : 2.747 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: 0.3533 time to fit residues: 195.4673 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 : 2.555 ------------------------------------------------------------------------------- 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 = 0.187524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.150717 restraints weight = 35932.110| |-----------------------------------------------------------------------------| 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: 0.6944 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 6.58943 ( 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 : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.6264 (pptt) cc_final: 0.5722 (mmtp) REVERT: D 263 LEU cc_start: 0.7783 (tp) cc_final: 0.7543 (pp) REVERT: D 437 ASP cc_start: 0.8177 (t0) cc_final: 0.7735 (t0) REVERT: D 492 MET cc_start: 0.6639 (ttm) cc_final: 0.6343 (ttm) REVERT: D 508 GLN cc_start: 0.5993 (OUTLIER) cc_final: 0.5351 (mp10) REVERT: D 538 MET cc_start: 0.5013 (ttm) cc_final: 0.4472 (mtp) REVERT: M 256 ASP cc_start: 0.7929 (t0) cc_final: 0.7674 (m-30) REVERT: M 381 ASN cc_start: 0.7584 (t0) cc_final: 0.7301 (t0) REVERT: M 491 MET cc_start: 0.7609 (tpp) cc_final: 0.7139 (tpp) REVERT: N 223 GLU cc_start: 0.3391 (tp30) cc_final: 0.1493 (tt0) REVERT: N 375 ARG cc_start: 0.4406 (tmt170) cc_final: 0.3201 (tpt90) REVERT: N 478 ARG cc_start: 0.7979 (mtm180) cc_final: 0.7130 (mtp180) REVERT: N 492 MET cc_start: 0.7901 (tpt) cc_final: 0.7277 (ttt) REVERT: N 576 LEU cc_start: 0.6679 (mp) cc_final: 0.6017 (pp) REVERT: N 651 GLU cc_start: 0.7247 (tt0) cc_final: 0.5899 (pm20) REVERT: O 19 ASP cc_start: 0.7662 (t0) cc_final: 0.7377 (t0) REVERT: O 98 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6701 (tm-30) REVERT: O 268 ARG cc_start: 0.7652 (ptp90) cc_final: 0.7010 (ptp90) REVERT: O 362 LYS cc_start: 0.8231 (tmmt) cc_final: 0.7953 (ttpt) REVERT: O 480 ILE cc_start: 0.8059 (mt) cc_final: 0.7844 (mt) REVERT: O 600 TRP cc_start: 0.6459 (t60) cc_final: 0.5452 (t60) REVERT: L 497 ARG cc_start: 0.8535 (tpt90) cc_final: 0.8199 (tpt90) outliers start: 35 outliers final: 23 residues processed: 313 average time/residue: 0.3578 time to fit residues: 169.9211 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 : 2.404 ------------------------------------------------------------------------------- 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: 0.4980 chunk 19 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 217 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 230 optimal weight: 30.0000 chunk 164 optimal weight: 0.0980 chunk 262 optimal weight: 0.0000 chunk 184 optimal weight: 0.6980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN D 290 HIS 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 = 0.4519 r_free = 0.4519 target = 0.192295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.155679 restraints weight = 35541.513| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 3.58 r_work: 0.3894 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 23048 Z= 0.113 Angle : 0.573 11.633 31266 Z= 0.295 Chirality : 0.046 0.231 3642 Planarity : 0.004 0.076 3983 Dihedral : 7.021 151.329 3245 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.29 % Allowed : 12.20 % Favored : 86.51 % 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: -1.38 (0.15), residues: 2916 helix: -0.30 (0.18), residues: 891 sheet: -1.37 (0.25), residues: 423 loop : -1.10 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 293 HIS 0.014 0.001 HIS D 290 PHE 0.016 0.001 PHE D 243 TYR 0.026 0.001 TYR O 130 ARG 0.003 0.000 ARG N 601 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 698) hydrogen bonds : angle 5.91638 ( 1938) covalent geometry : bond 0.00249 (23048) covalent geometry : angle 0.57328 (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: 31 poor density : 285 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.6329 (pptt) cc_final: 0.5709 (mmtp) REVERT: D 263 LEU cc_start: 0.7834 (tp) cc_final: 0.7585 (pp) REVERT: D 452 ARG cc_start: 0.6343 (ttp80) cc_final: 0.5174 (ttp80) REVERT: M 163 SER cc_start: 0.7703 (m) cc_final: 0.7337 (t) REVERT: M 256 ASP cc_start: 0.7979 (t0) cc_final: 0.7643 (m-30) REVERT: M 268 ARG cc_start: 0.6792 (tpm170) cc_final: 0.6582 (tpm170) REVERT: M 381 ASN cc_start: 0.7558 (t0) cc_final: 0.7239 (t0) REVERT: M 491 MET cc_start: 0.7385 (tpp) cc_final: 0.7009 (tpp) REVERT: M 492 MET cc_start: 0.7161 (tpp) cc_final: 0.6936 (tpp) REVERT: N 225 LYS cc_start: 0.7761 (pttp) cc_final: 0.7444 (pptt) REVERT: N 297 TYR cc_start: 0.1862 (m-80) cc_final: 0.1656 (m-80) REVERT: N 437 ASP cc_start: 0.5487 (m-30) cc_final: 0.4887 (p0) REVERT: N 492 MET cc_start: 0.7762 (tpt) cc_final: 0.7263 (ttt) REVERT: N 576 LEU cc_start: 0.6690 (mp) cc_final: 0.6035 (pp) REVERT: N 651 GLU cc_start: 0.7317 (tt0) cc_final: 0.5734 (pm20) REVERT: N 672 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8663 (pm20) REVERT: O 98 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6588 (tm-30) REVERT: O 362 LYS cc_start: 0.8310 (tmmt) cc_final: 0.7949 (ttpp) REVERT: O 600 TRP cc_start: 0.6601 (t60) cc_final: 0.6012 (t60) REVERT: L 69 GLN cc_start: 0.8230 (mt0) cc_final: 0.7726 (mp-120) REVERT: L 497 ARG cc_start: 0.8330 (tpt90) cc_final: 0.8090 (tpt90) outliers start: 31 outliers final: 15 residues processed: 309 average time/residue: 0.3464 time to fit residues: 165.2142 Evaluate side-chains 262 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 246 time to evaluate : 2.832 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 149 optimal weight: 6.9990 chunk 278 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.182860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.145858 restraints weight = 36658.214| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 3.79 r_work: 0.3751 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 23048 Z= 0.297 Angle : 0.751 11.444 31266 Z= 0.387 Chirality : 0.052 0.237 3642 Planarity : 0.006 0.078 3983 Dihedral : 7.610 152.537 3245 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.21 % Allowed : 14.74 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 2916 helix: -0.70 (0.17), residues: 881 sheet: -1.58 (0.25), residues: 408 loop : -1.45 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP N 600 HIS 0.015 0.002 HIS L 162 PHE 0.028 0.003 PHE L 378 TYR 0.037 0.003 TYR O 130 ARG 0.008 0.001 ARG L 485 Details of bonding type rmsd hydrogen bonds : bond 0.05228 ( 698) hydrogen bonds : angle 6.08138 ( 1938) covalent geometry : bond 0.00724 (23048) covalent geometry : angle 0.75052 (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 323 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 246 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8209 (t) cc_final: 0.7461 (m) REVERT: D 263 LEU cc_start: 0.7650 (tp) cc_final: 0.7431 (pp) REVERT: D 419 MET cc_start: 0.7286 (mtp) cc_final: 0.6937 (mtp) REVERT: D 508 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5512 (mp10) REVERT: M 90 ILE cc_start: 0.2768 (OUTLIER) cc_final: 0.2533 (pt) REVERT: M 381 ASN cc_start: 0.7876 (t0) cc_final: 0.7524 (t0) REVERT: M 447 GLU cc_start: 0.6378 (pp20) cc_final: 0.5319 (pp20) REVERT: M 480 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7382 (mp) REVERT: M 491 MET cc_start: 0.7566 (tpp) cc_final: 0.7111 (tpp) REVERT: N 225 LYS cc_start: 0.7882 (pttp) cc_final: 0.7635 (pptt) REVERT: N 269 GLN cc_start: 0.4959 (tp-100) cc_final: 0.4513 (tm-30) REVERT: N 297 TYR cc_start: 0.2049 (m-80) cc_final: 0.1670 (m-80) REVERT: N 492 MET cc_start: 0.7977 (tpt) cc_final: 0.7408 (ttt) REVERT: N 560 MET cc_start: 0.5088 (pmm) cc_final: 0.3791 (mtm) REVERT: N 576 LEU cc_start: 0.6790 (mp) cc_final: 0.6104 (pp) REVERT: N 651 GLU cc_start: 0.7396 (tt0) cc_final: 0.5781 (pm20) REVERT: O 98 GLU cc_start: 0.7601 (tm-30) cc_final: 0.6887 (tm-30) REVERT: O 497 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7035 (tpt170) REVERT: O 579 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6705 (p0) REVERT: O 600 TRP cc_start: 0.6485 (t60) cc_final: 0.5876 (t60) outliers start: 77 outliers final: 43 residues processed: 306 average time/residue: 0.3462 time to fit residues: 164.4282 Evaluate side-chains 268 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 2.729 ------------------------------------------------------------------------------- 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 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 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 369 SER 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 249 SER 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 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 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 662 TYR 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: 0.8980 chunk 142 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 175 optimal weight: 0.3980 chunk 263 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 271 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 49 GLN 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 = 0.4483 r_free = 0.4483 target = 0.188601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.151781 restraints weight = 35988.333| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 3.79 r_work: 0.3831 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23048 Z= 0.120 Angle : 0.583 9.322 31266 Z= 0.300 Chirality : 0.047 0.210 3642 Planarity : 0.004 0.077 3983 Dihedral : 7.110 153.068 3245 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.17 % Allowed : 16.91 % Favored : 80.92 % 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: -1.52 (0.15), residues: 2916 helix: -0.37 (0.18), residues: 899 sheet: -1.35 (0.25), residues: 407 loop : -1.26 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP N 600 HIS 0.010 0.001 HIS N 670 PHE 0.025 0.001 PHE O 378 TYR 0.022 0.001 TYR O 130 ARG 0.004 0.000 ARG M 443 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 698) hydrogen bonds : angle 5.62915 ( 1938) covalent geometry : bond 0.00280 (23048) covalent geometry : angle 0.58333 (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 314 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8333 (t) cc_final: 0.7551 (m) REVERT: D 133 GLN cc_start: 0.8236 (mt0) cc_final: 0.7701 (pp30) REVERT: D 135 LYS cc_start: 0.6609 (pptt) cc_final: 0.6081 (mmtp) REVERT: D 263 LEU cc_start: 0.7625 (tp) cc_final: 0.7401 (pp) REVERT: D 508 GLN cc_start: 0.6025 (OUTLIER) cc_final: 0.5500 (mp10) REVERT: M 381 ASN cc_start: 0.7716 (t0) cc_final: 0.7321 (t0) REVERT: M 447 GLU cc_start: 0.6430 (pp20) cc_final: 0.5566 (pp20) REVERT: M 491 MET cc_start: 0.7389 (tpp) cc_final: 0.6891 (tpp) REVERT: N 215 TYR cc_start: 0.5407 (m-80) cc_final: 0.5202 (m-80) REVERT: N 225 LYS cc_start: 0.7919 (pttp) cc_final: 0.7668 (pptt) REVERT: N 297 TYR cc_start: 0.2400 (m-80) cc_final: 0.2017 (m-80) REVERT: N 375 ARG cc_start: 0.4485 (OUTLIER) cc_final: 0.3132 (tpt90) REVERT: N 419 MET cc_start: 0.2763 (mmt) cc_final: 0.2065 (mmt) REVERT: N 437 ASP cc_start: 0.5766 (m-30) cc_final: 0.5143 (p0) REVERT: N 492 MET cc_start: 0.7712 (tpt) cc_final: 0.7345 (ttt) REVERT: N 560 MET cc_start: 0.4758 (pmm) cc_final: 0.4037 (mtt) REVERT: N 576 LEU cc_start: 0.6802 (mp) cc_final: 0.6091 (pp) REVERT: N 651 GLU cc_start: 0.7343 (tt0) cc_final: 0.5644 (pm20) REVERT: O 98 GLU cc_start: 0.7494 (tm-30) cc_final: 0.6796 (tm-30) REVERT: O 261 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7707 (mp) REVERT: O 497 ARG cc_start: 0.7144 (ttm-80) cc_final: 0.6757 (ttm-80) REVERT: O 579 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6552 (p0) REVERT: O 600 TRP cc_start: 0.6556 (t60) cc_final: 0.5886 (t60) REVERT: O 651 GLU cc_start: 0.4990 (pp20) cc_final: 0.3668 (pt0) REVERT: L 79 LEU cc_start: 0.7219 (tt) cc_final: 0.6546 (mp) REVERT: L 419 MET cc_start: 0.8550 (mmm) cc_final: 0.8335 (mmt) outliers start: 52 outliers final: 28 residues processed: 306 average time/residue: 0.3552 time to fit residues: 166.7993 Evaluate side-chains 269 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 126 LEU 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 214 VAL Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 432 ILE Chi-restraints excluded: chain M residue 438 SER 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 367 LEU Chi-restraints excluded: chain N residue 369 SER Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 375 ARG 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 218 THR Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain O residue 261 LEU Chi-restraints excluded: chain O residue 469 SER Chi-restraints excluded: chain 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 218 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 684 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 100 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 275 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.186882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.150072 restraints weight = 35975.465| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 3.84 r_work: 0.3813 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23048 Z= 0.152 Angle : 0.600 9.268 31266 Z= 0.305 Chirality : 0.047 0.218 3642 Planarity : 0.004 0.074 3983 Dihedral : 7.117 150.966 3245 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.21 % Allowed : 16.99 % Favored : 79.80 % 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: -1.49 (0.15), residues: 2916 helix: -0.34 (0.18), residues: 897 sheet: -1.42 (0.25), residues: 392 loop : -1.23 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP N 600 HIS 0.011 0.001 HIS L 162 PHE 0.019 0.002 PHE O 378 TYR 0.016 0.001 TYR O 130 ARG 0.007 0.000 ARG N 601 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 698) hydrogen bonds : angle 5.53965 ( 1938) covalent geometry : bond 0.00369 (23048) covalent geometry : angle 0.59988 (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 328 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 251 time to evaluate : 2.402 Fit side-chains revert: symmetry clash REVERT: D 52 SER cc_start: 0.8353 (t) cc_final: 0.7571 (m) REVERT: D 98 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7439 (tm-30) REVERT: D 133 GLN cc_start: 0.8289 (mt0) cc_final: 0.7894 (pp30) REVERT: D 263 LEU cc_start: 0.7656 (tp) cc_final: 0.7434 (pp) REVERT: D 452 ARG cc_start: 0.6588 (ttp80) cc_final: 0.5568 (mtp85) REVERT: D 508 GLN cc_start: 0.6147 (OUTLIER) cc_final: 0.5496 (mp10) REVERT: M 263 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6913 (mt) REVERT: M 381 ASN cc_start: 0.7897 (t0) cc_final: 0.7483 (t0) REVERT: M 447 GLU cc_start: 0.6332 (pp20) cc_final: 0.5549 (pp20) REVERT: M 491 MET cc_start: 0.7403 (tpp) cc_final: 0.6820 (tpp) REVERT: N 49 GLN cc_start: 0.2851 (OUTLIER) cc_final: 0.2378 (pm20) REVERT: N 215 TYR cc_start: 0.5389 (m-80) cc_final: 0.5166 (m-80) REVERT: N 225 LYS cc_start: 0.7944 (pttp) cc_final: 0.7702 (pptt) REVERT: N 297 TYR cc_start: 0.2487 (m-80) cc_final: 0.2114 (m-80) REVERT: N 375 ARG cc_start: 0.4370 (OUTLIER) cc_final: 0.2998 (tpt90) REVERT: N 419 MET cc_start: 0.2938 (mmt) cc_final: 0.2196 (mmt) REVERT: N 437 ASP cc_start: 0.5773 (m-30) cc_final: 0.5185 (p0) REVERT: N 492 MET cc_start: 0.7725 (tpt) cc_final: 0.7363 (ttt) REVERT: N 560 MET cc_start: 0.4716 (pmm) cc_final: 0.4034 (mtt) REVERT: N 576 LEU cc_start: 0.6733 (mp) cc_final: 0.5949 (pp) REVERT: N 651 GLU cc_start: 0.7326 (tt0) cc_final: 0.5973 (pm20) REVERT: O 98 GLU cc_start: 0.7555 (tm-30) cc_final: 0.6838 (tm-30) REVERT: O 126 LEU cc_start: 0.8296 (tt) cc_final: 0.7944 (pp) REVERT: O 261 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7780 (mp) REVERT: O 338 ILE cc_start: 0.7808 (mp) cc_final: 0.7299 (tp) REVERT: O 497 ARG cc_start: 0.7255 (ttm-80) cc_final: 0.6849 (ttm-80) REVERT: O 579 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6661 (p0) REVERT: O 600 TRP cc_start: 0.6383 (t60) cc_final: 0.5745 (t60) REVERT: O 651 GLU cc_start: 0.4964 (pp20) cc_final: 0.3678 (pt0) REVERT: L 69 GLN cc_start: 0.8313 (mt0) cc_final: 0.7932 (mp-120) REVERT: L 80 LEU cc_start: 0.5696 (OUTLIER) cc_final: 0.5224 (tt) REVERT: L 247 GLU cc_start: 0.7842 (pm20) cc_final: 0.7599 (mp0) REVERT: L 545 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7306 (ttm110) outliers start: 77 outliers final: 45 residues processed: 314 average time/residue: 0.3331 time to fit residues: 163.8926 Evaluate side-chains 280 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 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 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 432 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 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 369 SER 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 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 218 THR Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain O residue 261 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 579 ASP Chi-restraints excluded: chain O residue 650 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 540 MET 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: 10.0000 chunk 90 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.183036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.145221 restraints weight = 36382.177| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 4.00 r_work: 0.3767 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 23048 Z= 0.231 Angle : 0.691 9.311 31266 Z= 0.353 Chirality : 0.050 0.200 3642 Planarity : 0.005 0.075 3983 Dihedral : 7.434 151.302 3245 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.58 % Allowed : 17.91 % Favored : 78.51 % 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: -1.72 (0.15), residues: 2916 helix: -0.53 (0.17), residues: 893 sheet: -1.52 (0.25), residues: 405 loop : -1.37 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP N 600 HIS 0.013 0.002 HIS L 162 PHE 0.022 0.002 PHE L 440 TYR 0.021 0.002 TYR L 215 ARG 0.010 0.001 ARG N 601 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 698) hydrogen bonds : angle 5.71783 ( 1938) covalent geometry : bond 0.00562 (23048) covalent geometry : angle 0.69123 (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 326 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 240 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8054 (t) cc_final: 0.7269 (m) REVERT: D 98 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7595 (tm-30) REVERT: D 133 GLN cc_start: 0.8255 (mt0) cc_final: 0.7768 (pp30) REVERT: D 135 LYS cc_start: 0.6787 (pptt) cc_final: 0.6303 (mmtp) REVERT: D 263 LEU cc_start: 0.7722 (tp) cc_final: 0.7483 (pp) REVERT: D 452 ARG cc_start: 0.6844 (ttp80) cc_final: 0.5834 (mtp85) REVERT: D 491 MET cc_start: 0.8059 (mmm) cc_final: 0.7283 (mmm) REVERT: D 508 GLN cc_start: 0.6210 (OUTLIER) cc_final: 0.5514 (mp10) REVERT: D 517 MET cc_start: 0.6618 (ttm) cc_final: 0.6390 (ttm) REVERT: D 538 MET cc_start: 0.4760 (ttm) cc_final: 0.4535 (ttm) REVERT: M 162 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6741 (m90) REVERT: M 381 ASN cc_start: 0.7938 (t0) cc_final: 0.7469 (t0) REVERT: M 447 GLU cc_start: 0.6259 (pp20) cc_final: 0.5224 (pp20) REVERT: N 215 TYR cc_start: 0.5219 (m-80) cc_final: 0.5007 (m-80) REVERT: N 225 LYS cc_start: 0.7950 (pttp) cc_final: 0.7694 (pptt) REVERT: N 269 GLN cc_start: 0.4512 (tp-100) cc_final: 0.4217 (tm-30) REVERT: N 375 ARG cc_start: 0.4201 (OUTLIER) cc_final: 0.2657 (tpt90) REVERT: N 437 ASP cc_start: 0.5899 (m-30) cc_final: 0.5114 (p0) REVERT: N 458 LEU cc_start: 0.4739 (pp) cc_final: 0.4475 (pp) REVERT: N 492 MET cc_start: 0.7792 (tpt) cc_final: 0.7411 (ttt) REVERT: N 576 LEU cc_start: 0.6674 (mp) cc_final: 0.5814 (pp) REVERT: N 651 GLU cc_start: 0.7518 (tt0) cc_final: 0.5792 (pm20) REVERT: O 98 GLU cc_start: 0.7723 (tm-30) cc_final: 0.6952 (tm-30) REVERT: O 126 LEU cc_start: 0.8215 (tt) cc_final: 0.7928 (pp) REVERT: O 497 ARG cc_start: 0.7317 (ttm-80) cc_final: 0.6809 (tpt170) REVERT: O 579 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6704 (p0) REVERT: O 600 TRP cc_start: 0.6450 (t60) cc_final: 0.5706 (t60) REVERT: O 651 GLU cc_start: 0.4820 (pp20) cc_final: 0.3551 (pt0) REVERT: L 69 GLN cc_start: 0.8442 (mt0) cc_final: 0.7988 (mp-120) REVERT: L 80 LEU cc_start: 0.5473 (OUTLIER) cc_final: 0.4956 (tt) REVERT: L 247 GLU cc_start: 0.7843 (pm20) cc_final: 0.7627 (mp0) REVERT: L 367 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6576 (tp) REVERT: L 545 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7514 (ttm110) outliers start: 86 outliers final: 54 residues processed: 313 average time/residue: 0.3380 time to fit residues: 166.7803 Evaluate side-chains 289 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 228 time to evaluate : 2.484 ------------------------------------------------------------------------------- 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 334 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 156 ASP 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 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 369 SER 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 564 ILE Chi-restraints excluded: chain N residue 605 VAL Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 218 THR Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 527 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 O residue 665 VAL Chi-restraints excluded: chain L residue 27 VAL 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 367 LEU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 517 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: 0.9980 chunk 252 optimal weight: 1.9990 chunk 220 optimal weight: 0.0020 chunk 73 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 chunk 257 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 172 optimal weight: 0.2980 chunk 189 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.188850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.147701 restraints weight = 35928.205| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 3.49 r_work: 0.3858 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 23048 Z= 0.109 Angle : 0.591 10.008 31266 Z= 0.300 Chirality : 0.046 0.185 3642 Planarity : 0.004 0.074 3983 Dihedral : 6.936 149.297 3245 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.79 % Allowed : 19.45 % Favored : 78.76 % 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: -1.37 (0.15), residues: 2916 helix: -0.23 (0.18), residues: 900 sheet: -1.37 (0.26), residues: 399 loop : -1.14 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 404 HIS 0.010 0.001 HIS N 670 PHE 0.022 0.001 PHE D 198 TYR 0.017 0.001 TYR O 130 ARG 0.010 0.000 ARG N 601 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 698) hydrogen bonds : angle 5.39340 ( 1938) covalent geometry : bond 0.00248 (23048) covalent geometry : angle 0.59057 (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 301 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8265 (t) cc_final: 0.7477 (m) REVERT: D 133 GLN cc_start: 0.8179 (mt0) cc_final: 0.7706 (pp30) REVERT: D 135 LYS cc_start: 0.6798 (pptt) cc_final: 0.6314 (mmtp) REVERT: D 263 LEU cc_start: 0.7728 (tp) cc_final: 0.7477 (pp) REVERT: D 385 TRP cc_start: 0.6891 (m-90) cc_final: 0.6662 (m-90) REVERT: D 452 ARG cc_start: 0.6525 (ttp80) cc_final: 0.5706 (mtp85) REVERT: D 491 MET cc_start: 0.7969 (mmm) cc_final: 0.7214 (mmm) REVERT: D 538 MET cc_start: 0.4832 (ttm) cc_final: 0.4546 (ttp) REVERT: M 256 ASP cc_start: 0.7769 (t0) cc_final: 0.7450 (m-30) REVERT: M 381 ASN cc_start: 0.7781 (t0) cc_final: 0.7316 (t0) REVERT: M 447 GLU cc_start: 0.6216 (pp20) cc_final: 0.5475 (pp20) REVERT: M 491 MET cc_start: 0.7304 (tpp) cc_final: 0.6803 (tpp) REVERT: N 375 ARG cc_start: 0.4262 (OUTLIER) cc_final: 0.3029 (tpt90) REVERT: N 419 MET cc_start: 0.3316 (mmt) cc_final: 0.2521 (mmt) REVERT: N 437 ASP cc_start: 0.5770 (m-30) cc_final: 0.5258 (p0) REVERT: N 492 MET cc_start: 0.7650 (tpt) cc_final: 0.7357 (ttt) REVERT: N 560 MET cc_start: 0.5264 (pmm) cc_final: 0.3662 (mtm) REVERT: N 576 LEU cc_start: 0.6564 (mp) cc_final: 0.5811 (pp) REVERT: N 648 MET cc_start: 0.1968 (tpp) cc_final: 0.1676 (tpp) REVERT: N 651 GLU cc_start: 0.7460 (tt0) cc_final: 0.6993 (tt0) REVERT: O 24 ASN cc_start: 0.7662 (t0) cc_final: 0.7346 (m-40) REVERT: O 126 LEU cc_start: 0.8166 (tt) cc_final: 0.7919 (pp) REVERT: O 497 ARG cc_start: 0.7043 (ttm-80) cc_final: 0.6470 (tpt170) REVERT: O 579 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6767 (p0) REVERT: O 600 TRP cc_start: 0.6613 (t60) cc_final: 0.5941 (t60) REVERT: O 651 GLU cc_start: 0.4714 (pp20) cc_final: 0.3465 (pt0) REVERT: L 66 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6470 (mm) REVERT: L 69 GLN cc_start: 0.8261 (mt0) cc_final: 0.7876 (mp-120) REVERT: L 79 LEU cc_start: 0.7139 (tt) cc_final: 0.6624 (mp) REVERT: L 80 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.5078 (tt) REVERT: L 247 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: L 297 TYR cc_start: 0.6812 (t80) cc_final: 0.6488 (t80) REVERT: L 545 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7268 (ttm110) outliers start: 43 outliers final: 29 residues processed: 296 average time/residue: 0.3494 time to fit residues: 162.5451 Evaluate side-chains 272 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 2.615 ------------------------------------------------------------------------------- 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 334 VAL Chi-restraints excluded: chain D residue 439 LEU 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 504 THR Chi-restraints excluded: chain M residue 556 VAL Chi-restraints excluded: chain M residue 617 LEU Chi-restraints excluded: chain M residue 670 HIS Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 369 SER 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 O residue 92 VAL Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 249 SER Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 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 247 GLU 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: 0.0970 chunk 31 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 35 optimal weight: 0.0570 chunk 4 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 3.4302 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.183580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.144560 restraints weight = 36358.056| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 3.64 r_work: 0.3788 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23048 Z= 0.215 Angle : 0.683 11.590 31266 Z= 0.347 Chirality : 0.049 0.207 3642 Planarity : 0.005 0.071 3983 Dihedral : 7.262 147.808 3245 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.21 % Allowed : 19.33 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.63 (0.15), residues: 2916 helix: -0.50 (0.17), residues: 909 sheet: -1.48 (0.25), residues: 413 loop : -1.28 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 231 HIS 0.013 0.002 HIS L 162 PHE 0.021 0.002 PHE L 440 TYR 0.016 0.002 TYR L 215 ARG 0.009 0.001 ARG L 106 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 698) hydrogen bonds : angle 5.58383 ( 1938) covalent geometry : bond 0.00521 (23048) covalent geometry : angle 0.68328 (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 292 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 239 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8064 (t) cc_final: 0.7281 (m) REVERT: D 133 GLN cc_start: 0.8296 (mt0) cc_final: 0.7797 (pp30) REVERT: D 135 LYS cc_start: 0.6816 (pptt) cc_final: 0.6384 (mmtp) REVERT: D 263 LEU cc_start: 0.7739 (tp) cc_final: 0.7497 (pp) REVERT: D 452 ARG cc_start: 0.6740 (ttp80) cc_final: 0.5828 (mtp85) REVERT: D 517 MET cc_start: 0.6616 (ttm) cc_final: 0.6343 (ttm) REVERT: M 381 ASN cc_start: 0.7969 (t0) cc_final: 0.7517 (t0) REVERT: M 441 TRP cc_start: 0.7398 (m100) cc_final: 0.6810 (m100) REVERT: M 491 MET cc_start: 0.7443 (tpp) cc_final: 0.6854 (tpp) REVERT: N 269 GLN cc_start: 0.4546 (tp-100) cc_final: 0.4202 (tm-30) REVERT: N 375 ARG cc_start: 0.4105 (OUTLIER) cc_final: 0.2428 (tpt90) REVERT: N 419 MET cc_start: 0.3288 (mmt) cc_final: 0.2456 (mmt) REVERT: N 437 ASP cc_start: 0.6160 (m-30) cc_final: 0.5433 (p0) REVERT: N 492 MET cc_start: 0.7826 (tpt) cc_final: 0.7356 (ttt) REVERT: N 560 MET cc_start: 0.5201 (pmm) cc_final: 0.3565 (mtm) REVERT: N 648 MET cc_start: 0.2188 (tpp) cc_final: 0.1903 (tpp) REVERT: O 19 ASP cc_start: 0.7531 (t0) cc_final: 0.7323 (t0) REVERT: O 126 LEU cc_start: 0.8186 (tt) cc_final: 0.7951 (pp) REVERT: O 464 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: O 497 ARG cc_start: 0.7270 (ttm-80) cc_final: 0.6706 (tpt170) REVERT: O 579 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6658 (p0) REVERT: O 600 TRP cc_start: 0.6482 (t60) cc_final: 0.5762 (t60) REVERT: O 651 GLU cc_start: 0.4797 (pp20) cc_final: 0.3592 (pt0) REVERT: L 69 GLN cc_start: 0.8409 (mt0) cc_final: 0.7991 (mp-120) REVERT: L 80 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5482 (tt) REVERT: L 247 GLU cc_start: 0.7921 (pm20) cc_final: 0.7678 (mp0) REVERT: L 482 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7348 (mttt) REVERT: L 545 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7417 (ttm110) outliers start: 53 outliers final: 41 residues processed: 282 average time/residue: 0.3531 time to fit residues: 154.7109 Evaluate side-chains 280 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 233 time to evaluate : 2.766 ------------------------------------------------------------------------------- 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 334 VAL Chi-restraints excluded: chain D residue 439 LEU 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 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 617 LEU Chi-restraints excluded: chain M residue 670 HIS Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 369 SER 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 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 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 464 TYR 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 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 501 ILE Chi-restraints excluded: chain L residue 517 MET Chi-restraints excluded: chain L residue 545 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 76 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 191 optimal weight: 0.2980 chunk 85 optimal weight: 0.1980 chunk 25 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 162 optimal weight: 0.4980 chunk 183 optimal weight: 0.7980 chunk 250 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.188455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.150226 restraints weight = 36285.891| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 3.95 r_work: 0.3823 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3621 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= 0.122 Angle : 0.622 11.627 31266 Z= 0.314 Chirality : 0.046 0.223 3642 Planarity : 0.004 0.070 3983 Dihedral : 6.933 145.786 3245 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.96 % Allowed : 19.49 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.18), residues: 907 sheet: -1.34 (0.25), residues: 409 loop : -1.16 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 293 HIS 0.012 0.001 HIS N 670 PHE 0.020 0.001 PHE L 378 TYR 0.022 0.001 TYR O 130 ARG 0.005 0.000 ARG N 601 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 698) hydrogen bonds : angle 5.35488 ( 1938) covalent geometry : bond 0.00289 (23048) covalent geometry : angle 0.62194 (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 284 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 237 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.8276 (t) cc_final: 0.7480 (m) REVERT: D 133 GLN cc_start: 0.8274 (mt0) cc_final: 0.7809 (pp30) REVERT: D 135 LYS cc_start: 0.6830 (pptt) cc_final: 0.6379 (mmtp) REVERT: D 263 LEU cc_start: 0.7734 (tp) cc_final: 0.7505 (pp) REVERT: D 385 TRP cc_start: 0.6895 (m-90) cc_final: 0.6639 (m-90) REVERT: D 402 GLU cc_start: 0.8941 (tt0) cc_final: 0.8675 (tp30) REVERT: D 452 ARG cc_start: 0.6580 (ttp80) cc_final: 0.5690 (mtp85) REVERT: D 491 MET cc_start: 0.8010 (mmm) cc_final: 0.7096 (mmm) REVERT: M 256 ASP cc_start: 0.7791 (t0) cc_final: 0.7483 (m-30) REVERT: M 381 ASN cc_start: 0.7904 (t0) cc_final: 0.7443 (t0) REVERT: M 447 GLU cc_start: 0.6101 (pp20) cc_final: 0.5205 (pp20) REVERT: M 491 MET cc_start: 0.7398 (tpp) cc_final: 0.6925 (tpp) REVERT: M 543 THR cc_start: 0.6703 (m) cc_final: 0.6267 (t) REVERT: N 225 LYS cc_start: 0.7851 (pptt) cc_final: 0.6136 (tttt) REVERT: N 375 ARG cc_start: 0.3938 (OUTLIER) cc_final: 0.2674 (tpt90) REVERT: N 419 MET cc_start: 0.3276 (mmt) cc_final: 0.2482 (mmt) REVERT: N 437 ASP cc_start: 0.6077 (m-30) cc_final: 0.5553 (p0) REVERT: N 458 LEU cc_start: 0.4684 (pp) cc_final: 0.4433 (pt) REVERT: N 492 MET cc_start: 0.7654 (tpt) cc_final: 0.7295 (ttt) REVERT: N 560 MET cc_start: 0.5133 (pmm) cc_final: 0.3501 (mtm) REVERT: N 648 MET cc_start: 0.1984 (tpp) cc_final: 0.1704 (tpp) REVERT: O 126 LEU cc_start: 0.8223 (tt) cc_final: 0.7999 (pp) REVERT: O 497 ARG cc_start: 0.7078 (ttm-80) cc_final: 0.6568 (tpt170) REVERT: O 579 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6788 (p0) REVERT: O 600 TRP cc_start: 0.6677 (t60) cc_final: 0.5985 (t60) REVERT: O 651 GLU cc_start: 0.4720 (pp20) cc_final: 0.3526 (pt0) REVERT: L 66 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6531 (mm) REVERT: L 69 GLN cc_start: 0.8335 (mt0) cc_final: 0.7963 (mp-120) REVERT: L 79 LEU cc_start: 0.7170 (tt) cc_final: 0.6673 (mp) REVERT: L 80 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5527 (tt) REVERT: L 247 GLU cc_start: 0.7945 (pm20) cc_final: 0.7666 (mp0) REVERT: L 297 TYR cc_start: 0.6810 (t80) cc_final: 0.6527 (t80) REVERT: L 361 ARG cc_start: 0.6558 (tpt170) cc_final: 0.5509 (mmm160) REVERT: L 482 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7236 (mttt) REVERT: L 545 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7382 (ttm110) outliers start: 47 outliers final: 35 residues processed: 281 average time/residue: 0.3364 time to fit residues: 147.8949 Evaluate side-chains 274 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 2.490 ------------------------------------------------------------------------------- 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 334 VAL Chi-restraints excluded: chain D residue 439 LEU 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 504 THR Chi-restraints excluded: chain M residue 556 VAL Chi-restraints excluded: chain M residue 617 LEU Chi-restraints excluded: chain M residue 670 HIS Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 369 SER Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 375 ARG Chi-restraints excluded: chain N residue 494 VAL Chi-restraints excluded: chain N residue 672 GLU Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 170 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 278 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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** O 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.180361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.142068 restraints weight = 36587.479| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 3.63 r_work: 0.3753 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 23048 Z= 0.295 Angle : 0.785 15.031 31266 Z= 0.402 Chirality : 0.052 0.280 3642 Planarity : 0.006 0.069 3983 Dihedral : 7.571 145.736 3245 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.37 % Allowed : 19.12 % Favored : 78.51 % 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: -1.90 (0.15), residues: 2916 helix: -0.75 (0.17), residues: 900 sheet: -1.59 (0.25), residues: 411 loop : -1.44 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 293 HIS 0.013 0.002 HIS L 162 PHE 0.029 0.003 PHE L 440 TYR 0.023 0.002 TYR L 215 ARG 0.009 0.001 ARG L 485 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 698) hydrogen bonds : angle 5.84484 ( 1938) covalent geometry : bond 0.00722 (23048) covalent geometry : angle 0.78547 (31266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11525.94 seconds wall clock time: 197 minutes 44.31 seconds (11864.31 seconds total)