Starting phenix.real_space_refine on Wed Nov 20 01:54:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wk0_37592/11_2024/8wk0_37592_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wk0_37592/11_2024/8wk0_37592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wk0_37592/11_2024/8wk0_37592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wk0_37592/11_2024/8wk0_37592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wk0_37592/11_2024/8wk0_37592_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wk0_37592/11_2024/8wk0_37592_trim.cif" } resolution = 3.34 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= 0.049 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: 7 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 68 5.16 5 C 17123 2.51 5 N 4620 2.21 5 O 5137 1.98 5 H 26743 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 53711 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6360 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 9474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 9474 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 26, 'TRANS': 575} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 9654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 9654 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 29, 'TRANS': 600} Chain breaks: 4 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 106 Chain: "N" Number of atoms: 8024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8024 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 24, 'TRANS': 517} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 146 Chain: "O" Number of atoms: 10130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 10130 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 30, 'TRANS': 626} Chain breaks: 3 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 4, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "L" Number of atoms: 9909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 9909 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 30, 'TRANS': 613} Chain breaks: 3 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 100 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: "D" 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: "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: "N" 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: 24.17, per 1000 atoms: 0.45 Number of scatterers: 53711 At special positions: 0 Unit cell: (118.336, 143.079, 152.761, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 68 16.00 P 15 15.00 Mg 5 11.99 O 5137 8.00 N 4620 7.00 C 17123 6.00 H 26743 1.00 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: 13.36 Conformation dependent library (CDL) restraints added in 4.1 seconds 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6388 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 22 sheets defined 36.1% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'A' and resid 78 through 83 removed outlier: 4.079A pdb=" N VAL A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.939A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 removed outlier: 4.257A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 248 through 268 removed outlier: 3.913A pdb=" N ASN A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 Processing helix chain 'A' and resid 420 through 442 removed outlier: 3.510A pdb=" N LEU A 424 " --> pdb=" O PRO A 420 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.688A pdb=" N THR A 463 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 484 removed outlier: 4.449A pdb=" N ASP A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 476 " --> pdb=" O ILE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 519 through 529 removed outlier: 3.600A pdb=" N LEU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 removed outlier: 3.942A pdb=" N MET A 538 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 122 through 131 Processing helix chain 'D' and resid 154 through 161 Processing helix chain 'D' and resid 172 through 184 Processing helix chain 'D' and resid 203 through 207 Processing helix chain 'D' and resid 234 through 244 Processing helix chain 'D' and resid 248 through 269 removed outlier: 3.739A pdb=" N ASN D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.914A pdb=" N LEU D 279 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 299 removed outlier: 3.641A pdb=" N ALA D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 372 removed outlier: 3.633A pdb=" N LYS D 372 " --> pdb=" O ALA D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 377 Processing helix chain 'D' and resid 396 through 407 removed outlier: 4.192A pdb=" N LEU D 400 " --> pdb=" O ASP D 396 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER D 407 " --> pdb=" O THR D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 441 removed outlier: 4.615A pdb=" N ASP D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N THR D 426 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 430 " --> pdb=" O THR D 426 " (cutoff:3.500A) removed outlier: 3.829A 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 497 through 501 Processing helix chain 'D' and resid 502 through 507 Processing helix chain 'D' and resid 519 through 529 removed outlier: 3.574A pdb=" N ASN D 524 " --> pdb=" O SER D 520 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS D 525 " --> pdb=" O SER D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 544 removed outlier: 3.539A pdb=" N THR D 543 " --> pdb=" O MET D 540 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 544 " --> pdb=" O LEU D 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 540 through 544' Processing helix chain 'D' and resid 579 through 586 removed outlier: 3.672A pdb=" N ASN D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 601 removed outlier: 3.521A pdb=" N VAL D 596 " --> pdb=" O ASP D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 657 No H-bonds generated for 'chain 'D' and resid 655 through 657' Processing helix chain 'D' and resid 666 through 677 removed outlier: 3.883A pdb=" N GLU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 687 removed outlier: 3.561A pdb=" N GLN D 686 " --> pdb=" O PHE D 682 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 131 Processing helix chain 'M' and resid 155 through 161 removed outlier: 3.571A pdb=" N ARG M 161 " --> pdb=" O THR M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 185 removed outlier: 3.848A 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 Processing helix chain 'M' and resid 248 through 269 removed outlier: 3.659A pdb=" N ASN M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU M 266 " --> pdb=" O LYS M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 299 Processing helix chain 'M' and resid 311 through 315 Processing helix chain 'M' and resid 360 through 371 Processing helix chain 'M' and resid 373 through 375 No H-bonds generated for 'chain 'M' and resid 373 through 375' Processing helix chain 'M' and resid 376 through 381 Processing helix chain 'M' and resid 396 through 405 removed outlier: 4.092A pdb=" N LEU M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 423 through 442 removed outlier: 4.017A pdb=" N SER M 442 " --> pdb=" O SER M 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 464 removed outlier: 3.978A pdb=" N THR M 463 " --> pdb=" O GLU M 460 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR M 464 " --> pdb=" O ALA M 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 460 through 464' Processing helix chain 'M' and resid 472 through 484 Processing helix chain 'M' and resid 502 through 508 Processing helix chain 'M' and resid 519 through 528 removed outlier: 3.538A pdb=" N ARG M 523 " --> pdb=" O ASN M 519 " (cutoff:3.500A) Processing helix chain 'M' and resid 534 through 539 removed outlier: 3.788A pdb=" N GLY M 539 " --> pdb=" O GLU M 535 " (cutoff:3.500A) Processing helix chain 'M' and resid 540 through 544 removed outlier: 3.609A pdb=" N THR M 543 " --> pdb=" O MET M 540 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU M 544 " --> pdb=" O LEU M 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 540 through 544' Processing helix chain 'M' and resid 579 through 586 removed outlier: 4.144A pdb=" N ASN M 586 " --> pdb=" O ALA M 582 " (cutoff:3.500A) Processing helix chain 'M' and resid 592 through 603 removed outlier: 3.836A pdb=" N VAL M 596 " --> pdb=" O ASP M 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 666 through 677 removed outlier: 3.773A pdb=" N HIS M 670 " --> pdb=" O PRO M 666 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU M 677 " --> pdb=" O LEU M 673 " (cutoff:3.500A) Processing helix chain 'M' and resid 682 through 687 removed outlier: 4.446A pdb=" N GLN M 686 " --> pdb=" O PHE M 682 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 130 Processing helix chain 'N' and resid 155 through 161 Processing helix chain 'N' and resid 172 through 184 removed outlier: 3.889A 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 Processing helix chain 'N' and resid 248 through 269 removed outlier: 3.700A pdb=" N ASN N 252 " --> pdb=" O GLY N 248 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR N 259 " --> pdb=" O ILE N 255 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU N 260 " --> pdb=" O ASP N 256 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU N 261 " --> pdb=" O LYS N 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 288 through 299 removed outlier: 3.686A pdb=" N LEU N 292 " --> pdb=" O SER N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 373 Processing helix chain 'N' and resid 376 through 381 Processing helix chain 'N' and resid 396 through 405 Processing helix chain 'N' and resid 420 through 422 No H-bonds generated for 'chain 'N' and resid 420 through 422' Processing helix chain 'N' and resid 423 through 441 removed outlier: 3.620A pdb=" N TRP N 441 " --> pdb=" O ASP N 437 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 465 removed outlier: 3.856A pdb=" N TYR N 464 " --> pdb=" O GLU N 460 " (cutoff:3.500A) Processing helix chain 'N' and resid 472 through 484 Processing helix chain 'N' and resid 502 through 508 removed outlier: 4.143A pdb=" N GLN N 508 " --> pdb=" O THR N 504 " (cutoff:3.500A) Processing helix chain 'N' and resid 519 through 529 removed outlier: 3.925A pdb=" N ARG N 523 " --> pdb=" O ASN N 519 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN N 524 " --> pdb=" O SER N 520 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS N 525 " --> pdb=" O SER N 521 " (cutoff:3.500A) Processing helix chain 'N' and resid 535 through 539 Processing helix chain 'N' and resid 540 through 544 removed outlier: 3.648A pdb=" N THR N 543 " --> pdb=" O MET N 540 " (cutoff:3.500A) Processing helix chain 'N' and resid 579 through 586 removed outlier: 3.858A pdb=" N ASN N 586 " --> pdb=" O ALA N 582 " (cutoff:3.500A) Processing helix chain 'N' and resid 593 through 603 Processing helix chain 'N' and resid 666 through 677 removed outlier: 3.838A pdb=" N HIS N 670 " --> pdb=" O PRO N 666 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU N 672 " --> pdb=" O THR N 668 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU N 677 " --> pdb=" O LEU N 673 " (cutoff:3.500A) Processing helix chain 'N' and resid 680 through 687 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 Processing helix chain 'O' and resid 229 through 233 Processing helix chain 'O' and resid 234 through 243 Processing helix chain 'O' and resid 248 through 269 removed outlier: 4.020A pdb=" N ASN O 252 " --> pdb=" O GLY O 248 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG O 268 " --> pdb=" O GLN O 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 288 through 302 removed outlier: 3.519A pdb=" N LEU O 292 " --> pdb=" O SER O 288 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA O 299 " --> pdb=" O ASP O 295 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU O 300 " --> pdb=" O LEU O 296 " (cutoff:3.500A) 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 removed outlier: 4.101A pdb=" N LEU O 400 " --> pdb=" O ASP O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 423 through 442 removed outlier: 4.065A pdb=" N SER O 442 " --> pdb=" O SER O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 472 through 484 Processing helix chain 'O' and resid 502 through 507 Processing helix chain 'O' and resid 519 through 528 removed outlier: 3.664A pdb=" N ARG O 523 " --> pdb=" O ASN O 519 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN O 524 " --> pdb=" O SER O 520 " (cutoff:3.500A) Processing helix chain 'O' and resid 534 through 539 removed outlier: 3.885A pdb=" N GLY O 539 " --> pdb=" O GLU O 535 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 544 removed outlier: 3.705A pdb=" N THR O 543 " --> pdb=" O MET O 540 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU O 544 " --> pdb=" O LEU O 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 540 through 544' Processing helix chain 'O' and resid 579 through 585 removed outlier: 3.656A pdb=" N SER O 585 " --> pdb=" O THR O 581 " (cutoff:3.500A) Processing helix chain 'O' and resid 593 through 603 Processing helix chain 'O' and resid 655 through 657 No H-bonds generated for 'chain 'O' and resid 655 through 657' Processing helix chain 'O' and resid 666 through 677 removed outlier: 3.826A pdb=" N GLU O 677 " --> pdb=" O LEU O 673 " (cutoff:3.500A) Processing helix chain 'O' and resid 681 through 686 Processing helix chain 'L' and resid 73 through 75 No H-bonds generated for 'chain 'L' and resid 73 through 75' Processing helix chain 'L' and resid 122 through 131 Processing helix chain 'L' and resid 155 through 161 Processing helix chain 'L' and resid 172 through 185 removed outlier: 3.763A pdb=" N ILE L 180 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER L 185 " --> pdb=" O LEU L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 233 removed outlier: 3.652A pdb=" N LEU L 233 " --> pdb=" O TYR L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 244 Processing helix chain 'L' and resid 249 through 269 removed outlier: 4.048A pdb=" N ILE L 255 " --> pdb=" O ARG L 251 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP L 256 " --> pdb=" O ASN L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 301 Processing helix chain 'L' and resid 311 through 315 Processing helix chain 'L' and resid 360 through 373 Processing helix chain 'L' and resid 376 through 381 Processing helix chain 'L' and resid 396 through 406 removed outlier: 3.957A pdb=" N LEU L 400 " --> pdb=" O ASP L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 422 No H-bonds generated for 'chain 'L' and resid 420 through 422' Processing helix chain 'L' and resid 423 through 441 Processing helix chain 'L' and resid 472 through 488 removed outlier: 3.597A pdb=" N GLY L 476 " --> pdb=" O ILE L 472 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ARG L 485 " --> pdb=" O VAL L 481 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS L 486 " --> pdb=" O LYS L 482 " (cutoff:3.500A) removed outlier: 3.921A 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 Processing helix chain 'L' and resid 519 through 527 Processing helix chain 'L' and resid 579 through 584 Processing helix chain 'L' and resid 592 through 603 removed outlier: 4.093A pdb=" N VAL L 596 " --> pdb=" O ASP L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 667 through 676 removed outlier: 4.256A pdb=" N THR L 671 " --> pdb=" O GLU L 667 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU L 672 " --> pdb=" O THR L 668 " (cutoff:3.500A) Processing helix chain 'L' and resid 682 through 687 removed outlier: 3.532A pdb=" N ILE L 687 " --> pdb=" O PHE L 683 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.280A pdb=" N ARG A 26 " --> pdb=" O GLN A 18 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 29 current: chain 'A' and resid 62 through 70 removed outlier: 6.632A pdb=" N ASN A 62 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU A 97 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE A 64 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER A 91 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A 70 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N TRP A 89 " --> pdb=" O VAL A 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 104 through 106 current: chain 'D' and resid 25 through 28 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 28 current: chain 'D' and resid 61 through 71 removed outlier: 6.706A pdb=" N SER D 91 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL D 70 " --> pdb=" O TRP D 89 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N TRP D 89 " --> pdb=" O VAL D 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 89 through 94 current: chain 'O' and resid 25 through 28 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 25 through 28 current: chain 'O' and resid 61 through 71 removed outlier: 6.692A pdb=" N SER O 91 " --> pdb=" O SER O 68 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL O 70 " --> pdb=" O TRP O 89 " (cutoff:3.500A) removed outlier: 7.254A 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 89 through 94 current: chain 'L' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 24 through 29 current: chain 'L' and resid 61 through 71 removed outlier: 6.664A pdb=" N SER L 91 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL L 70 " --> pdb=" O TRP L 89 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N TRP L 89 " --> pdb=" O VAL L 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 154 removed outlier: 6.156A pdb=" N ALA A 151 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 456 " --> pdb=" O MET A 492 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL A 494 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 458 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 196 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 138 through 142 removed outlier: 5.901A pdb=" N SER D 139 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL D 153 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY D 141 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 163 through 165 removed outlier: 3.977A pdb=" N LEU D 493 " --> pdb=" O SER D 163 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL D 456 " --> pdb=" O MET D 492 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL D 494 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU D 458 " --> pdb=" O VAL D 494 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU D 459 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS D 213 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 224 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 216 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 512 through 514 Processing sheet with id=AA7, first strand: chain 'D' and resid 640 through 641 removed outlier: 4.248A pdb=" N SER D 640 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU D 653 " --> pdb=" O SER D 640 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL D 659 " --> pdb=" O ILE D 696 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 661 " --> pdb=" O SER D 694 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 16 through 19 removed outlier: 6.862A pdb=" N ARG M 26 " --> pdb=" O GLN M 18 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE M 90 " --> pdb=" O VAL M 27 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN M 69 " --> pdb=" O SER M 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 54 through 58 removed outlier: 4.416A pdb=" N ASN M 62 " --> pdb=" O GLU M 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 138 through 139 Processing sheet with id=AB2, first strand: chain 'M' and resid 141 through 143 removed outlier: 3.550A pdb=" N ASN M 142 " --> pdb=" O ILE M 563 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA M 164 " --> pdb=" O PHE M 513 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU M 493 " --> pdb=" O SER M 163 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE M 195 " --> pdb=" O SER M 412 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N PHE M 414 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL M 197 " --> pdb=" O PHE M 414 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU M 224 " --> pdb=" O VAL M 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 617 through 618 removed outlier: 4.194A pdb=" N LEU M 617 " --> pdb=" O ILE M 641 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE M 641 " --> pdb=" O LEU M 617 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 64 through 65 removed outlier: 3.527A pdb=" N HIS N 119 " --> pdb=" O ARG N 55 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 97 through 98 Processing sheet with id=AB6, first strand: chain 'N' and resid 137 through 139 Processing sheet with id=AB7, first strand: chain 'N' and resid 141 through 143 removed outlier: 3.687A pdb=" N MET N 560 " --> pdb=" O ILE N 551 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N SER N 163 " --> pdb=" O LEU N 493 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N SER N 495 " --> pdb=" O SER N 163 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL N 165 " --> pdb=" O SER N 495 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU N 454 " --> pdb=" O GLY N 490 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N MET N 492 " --> pdb=" O LEU N 454 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL N 456 " --> pdb=" O MET N 492 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL N 494 " --> pdb=" O VAL N 456 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU N 458 " --> pdb=" O VAL N 494 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE N 195 " --> pdb=" O SER N 412 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N PHE N 414 " --> pdb=" O ILE N 195 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL N 197 " --> pdb=" O PHE N 414 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS N 213 " --> pdb=" O ILE N 413 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP N 415 " --> pdb=" O LYS N 213 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR N 215 " --> pdb=" O ASP N 415 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU N 224 " --> pdb=" O VAL N 214 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS N 216 " --> pdb=" O LEU N 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 617 through 618 removed outlier: 3.644A pdb=" N SER N 640 " --> pdb=" O GLU N 653 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU N 650 " --> pdb=" O TYR N 662 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 150 through 154 removed outlier: 6.407A pdb=" N ALA O 151 " --> pdb=" O LEU O 140 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA O 164 " --> pdb=" O PHE O 513 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE O 196 " --> pdb=" O VAL O 457 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LYS O 213 " --> pdb=" O ILE O 413 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASP O 415 " --> pdb=" O LYS O 213 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR O 215 " --> pdb=" O ASP O 415 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS O 216 " --> pdb=" O LEU O 224 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 617 through 618 removed outlier: 4.085A pdb=" N LEU O 617 " --> pdb=" O ILE O 641 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER O 640 " --> pdb=" O GLU O 653 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 96 through 98 Processing sheet with id=AC3, first strand: chain 'L' and resid 150 through 154 removed outlier: 6.793A pdb=" N ALA L 151 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU L 493 " --> pdb=" O SER L 163 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY L 490 " --> pdb=" O LEU L 454 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL L 456 " --> pdb=" O GLY L 490 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE L 195 " --> pdb=" O SER L 412 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N PHE L 414 " --> pdb=" O ILE L 195 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL L 197 " --> pdb=" O PHE L 414 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS L 213 " --> pdb=" O ILE L 413 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASP L 415 " --> pdb=" O LYS L 213 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR L 215 " --> pdb=" O ASP L 415 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 616 through 618 removed outlier: 3.591A pdb=" N GLU L 651 " --> pdb=" O GLY L 642 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG L 692 " --> pdb=" O TYR L 663 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2442 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: 23.72 Time building geometry restraints manager: 15.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 26731 1.05 - 1.27: 4495 1.27 - 1.48: 10944 1.48 - 1.70: 11915 1.70 - 1.91: 119 Bond restraints: 54204 Sorted by residual: bond pdb=" C3' AGS M 701 " pdb=" C4' AGS M 701 " ideal model delta sigma weight residual 1.526 1.269 0.257 1.10e-02 8.26e+03 5.45e+02 bond pdb=" C3' AGS N 701 " pdb=" C4' AGS N 701 " ideal model delta sigma weight residual 1.526 1.270 0.256 1.10e-02 8.26e+03 5.41e+02 bond pdb=" C3' AGS D 701 " pdb=" C4' AGS D 701 " ideal model delta sigma weight residual 1.526 1.276 0.250 1.10e-02 8.26e+03 5.16e+02 bond pdb=" C3' AGS O 701 " pdb=" C4' AGS O 701 " ideal model delta sigma weight residual 1.526 1.276 0.250 1.10e-02 8.26e+03 5.15e+02 bond pdb=" C3' AGS L 701 " pdb=" C4' AGS L 701 " ideal model delta sigma weight residual 1.526 1.280 0.246 1.10e-02 8.26e+03 4.99e+02 ... (remaining 54199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 97738 2.51 - 5.02: 336 5.02 - 7.53: 27 7.53 - 10.05: 10 10.05 - 12.56: 11 Bond angle restraints: 98122 Sorted by residual: angle pdb=" N1 AGS N 701 " pdb=" C2 AGS N 701 " pdb=" N3 AGS N 701 " ideal model delta sigma weight residual 128.80 120.04 8.76 8.41e-01 1.41e+00 1.09e+02 angle pdb=" N1 AGS M 701 " pdb=" C2 AGS M 701 " pdb=" N3 AGS M 701 " ideal model delta sigma weight residual 128.80 120.12 8.68 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS D 701 " pdb=" C2 AGS D 701 " pdb=" N3 AGS D 701 " ideal model delta sigma weight residual 128.80 120.15 8.65 8.41e-01 1.41e+00 1.06e+02 angle pdb=" N1 AGS L 701 " pdb=" C2 AGS L 701 " pdb=" N3 AGS L 701 " ideal model delta sigma weight residual 128.80 120.16 8.64 8.41e-01 1.41e+00 1.05e+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 98117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.59: 24524 33.59 - 67.17: 839 67.17 - 100.76: 30 100.76 - 134.34: 2 134.34 - 167.93: 2 Dihedral angle restraints: 25397 sinusoidal: 13998 harmonic: 11399 Sorted by residual: 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 180.00 153.81 26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ARG A 161 " pdb=" C ARG A 161 " pdb=" N HIS A 162 " pdb=" CA HIS A 162 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" O1B AGS D 701 " pdb=" O3B AGS D 701 " pdb=" PB AGS D 701 " pdb=" PG AGS D 701 " ideal model delta sinusoidal sigma weight residual 68.91 -99.02 167.93 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 25394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3356 0.051 - 0.101: 698 0.101 - 0.152: 224 0.152 - 0.203: 12 0.203 - 0.253: 4 Chirality restraints: 4294 Sorted by residual: 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 -2.42 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C2' AGS D 701 " pdb=" C1' AGS D 701 " pdb=" C3' AGS D 701 " pdb=" O2' AGS D 701 " both_signs ideal model delta sigma weight residual False -2.67 -2.45 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C2' AGS N 701 " pdb=" C1' AGS N 701 " pdb=" C3' AGS N 701 " pdb=" O2' AGS N 701 " both_signs ideal model delta sigma weight residual False -2.67 -2.46 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 4291 not shown) Planarity restraints: 8027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 56 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO D 57 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 57 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 57 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 373 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO D 374 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 374 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 374 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 75 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO D 76 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 76 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 76 " -0.027 5.00e-02 4.00e+02 ... (remaining 8024 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 952 2.07 - 2.71: 89618 2.71 - 3.34: 148864 3.34 - 3.97: 186049 3.97 - 4.60: 296209 Nonbonded interactions: 721692 Sorted by model distance: nonbonded pdb=" HE2 HIS O 201 " pdb=" OE2 GLU O 460 " model vdw 1.442 2.450 nonbonded pdb=" H ARG L 545 " pdb=" OE1 GLU L 548 " model vdw 1.482 2.450 nonbonded pdb=" O ILE L 14 " pdb=" H ASP L 30 " model vdw 1.482 2.450 nonbonded pdb=" OD1 ASP N 373 " pdb=" H ARG N 375 " model vdw 1.512 2.450 nonbonded pdb=" O LYS L 216 " pdb=" H LEU L 226 " model vdw 1.532 2.450 ... (remaining 721687 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 'D' and ((resid 18 and (name N or name CA or name C or name O or name CB \ or name HA )) or (resid 19 through 21 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 22 through 23 or (resid 24 through \ 30 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or (resid 49 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HE21 or name HE22)) or resid 50 through 53 or (resid 54 thr \ ough 56 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 57 or (resid 58 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 59 or (resid 60 through 62 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 65 or (resid 66 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 67 through 68 or (resid 69 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 70 throu \ gh 73 or (resid 89 and (name N or name CA or name C or name O or name CB or name \ HA )) or (resid 90 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 91 or (resid 92 through 93 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 94 through 97 or (r \ esid 98 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 99 or (resid 100 through 101 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 102 or (resid 103 through 106 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 107 or (resid 108 through 111 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or (resid 112 and (name N or name CA or name \ C or name O or name CB or name HA )) or (resid 113 through 114 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 115 or (r \ esid 116 through 120 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 121 through 122 or (resid 123 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 124 or (resid 1 \ 25 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 126 or (resid 127 through 128 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or (resid 136 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or nam \ e HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) \ or resid 137 through 185 or (resid 186 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or (resid 194 and (name N or name CA or nam \ e C or name O or name CB or name HA )) or resid 195 through 269 or (resid 283 an \ d (name N or name CA or name C or name O or name CB or name OG1 or name CG2 or n \ ame HA or name HB or name HG1 or name HG21 or name HG22 or name HG23)) or resid \ 284 through 405 or (resid 410 and (name N or name CA or name C or name O or name \ CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 411 thr \ ough 440 or (resid 441 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 453 through 531 or (resid 532 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 533 or (resid \ 534 through 535 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 536 through 539 or (resid 540 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 541 through 570 or \ (resid 571 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 572 through 678 or (resid 679 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 680 or (resid 681 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 682 through 696 or resid 701 through 702)) selection = (chain 'L' and ((resid 18 and (name N or name CA or name C or name O or name CB \ or name HA )) or (resid 19 through 21 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 22 through 23 or (resid 24 through \ 30 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or (resid 49 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HE21 or name HE22)) or resid 50 through 53 or (resid 54 thr \ ough 56 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 57 or (resid 58 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 59 or (resid 60 through 62 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 65 or (resid 66 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 67 through 68 or (resid 69 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 70 throu \ gh 73 or (resid 89 and (name N or name CA or name C or name O or name CB or name \ HA )) or (resid 90 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 91 or (resid 92 through 93 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 94 through 97 or (r \ esid 98 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 99 or (resid 100 through 101 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 102 or (resid 103 through 106 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 107 or (resid 108 through 111 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or (resid 112 and (name N or name CA or name \ C or name O or name CB or name HA )) or (resid 113 through 114 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 115 or (r \ esid 116 through 120 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 121 through 122 or (resid 123 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 124 or (resid 1 \ 25 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 126 or (resid 127 through 128 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or (resid 136 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or nam \ e HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) \ or resid 137 through 185 or (resid 186 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or (resid 194 and (name N or name CA or nam \ e C or name O or name CB or name HA )) or resid 195 through 200 or (resid 201 an \ d (name N or name CA or name C or name O or name CB or name CG or name ND1 or na \ me CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or n \ ame HD2 or name HE1 or name HE2)) or resid 202 through 269 or (resid 283 and (na \ me N or name CA or name C or name O or name CB or name OG1 or name CG2 or name H \ A or name HB or name HG1 or name HG21 or name HG22 or name HG23)) or resid 284 t \ hrough 301 or (resid 302 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 332 through \ 336 or (resid 359 and (name N or name CA or name C or name O or name CB or name \ CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD21 or na \ me HD22)) or resid 360 through 405 or (resid 410 and (name N or name CA or name \ C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG \ )) or resid 411 through 440 or (resid 441 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 453 through 531 or (resid 532 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 533 or (resid 534 through 535 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 536 through 539 or (resid 540 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 541 through 570 or (resid 571 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 572 through 606 or (resid 607 and (name N o \ r name CA or name C or name O or name CB or name OG or name HA or name HB2 or na \ me HB3 or name HG )) or resid 637 through 696 or resid 701 through 702)) selection = (chain 'M' and ((resid 18 and (name N or name CA or name C or name O or name CB \ or name HA )) or (resid 19 through 21 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 22 through 23 or (resid 24 through \ 30 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or (resid 49 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HE21 or name HE22)) or resid 50 through 53 or (resid 54 thr \ ough 56 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 57 or (resid 58 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 59 or (resid 60 through 62 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 65 or (resid 66 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 67 through 68 or (resid 69 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 70 throu \ gh 73 or (resid 89 and (name N or name CA or name C or name O or name CB or name \ HA )) or (resid 90 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 91 or (resid 92 through 93 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 94 through 97 or (r \ esid 98 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 99 or (resid 100 through 101 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 102 or (resid 103 through 106 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 107 or (resid 108 through 111 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or (resid 112 and (name N or name CA or name \ C or name O or name CB or name HA )) or (resid 113 through 114 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 115 or (r \ esid 116 through 120 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 121 through 124 or (resid 125 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 126 or (resid 1 \ 27 through 128 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 129 through 130 or (resid 136 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 137 through 173 \ or (resid 174 and (name N or name CA or name C or name O or name CB or name OG o \ r name H or name HA or name HB2 or name HB3)) or resid 175 through 185 or (resid \ 186 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or (resid 194 and (name N or name CA or name C or name O or name CB or name H \ A )) or resid 195 through 269 or (resid 283 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or n \ ame HG21 or name HG22 or name HG23)) or resid 284 through 301 or (resid 302 and \ (name N or name CA or name C or name O or name CB or name OG or name HA or name \ HB2 or name HB3 or name HG )) or resid 332 through 336 or (resid 359 and (name N \ or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or \ name HA or name HB2 or name HB3 or name HD21 or name HD22)) or resid 360 throug \ h 405 or (resid 410 and (name N or name CA or name C or name O or name CB or nam \ e OG or name HA or name HB2 or name HB3 or name HG )) or resid 411 through 440 o \ r (resid 441 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 453 through 531 or (resid 532 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 533 or (resid 534 throu \ gh 535 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 536 through 539 or (resid 540 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 541 through 606 or (resid 607 \ and (name N or name CA or name C or name O or name CB or name OG or name HA or \ name HB2 or name HB3 or name HG )) or resid 637 through 678 or (resid 679 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 680 or (resid 681 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 682 through 696 or resid 701 through 702)) selection = (chain 'N' and (resid 18 through 122 or (resid 123 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 124 through 129 or (re \ sid 130 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 136 through 173 or (resid 174 and (name N or name CA or name C or \ name O or name CB or name OG or name H or name HA or name HB2 or name HB3)) or \ resid 175 through 336 or (resid 359 and (name N or name CA or name C or name O o \ r name CB or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 \ or name HD21 or name HD22)) or resid 360 through 606 or (resid 607 and (name N o \ r name CA or name C or name O or name CB or name OG or name HA or name HB2 or na \ me HB3 or name HG )) or resid 637 through 678 or (resid 679 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 680 or (resid \ 681 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 682 through 696 or resid 701 through 702)) selection = (chain 'O' and ((resid 18 and (name N or name CA or name C or name O or name CB \ or name HA )) or (resid 19 through 21 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 22 through 23 or (resid 24 through \ 30 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or (resid 49 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HE21 or name HE22)) or resid 50 through 53 or (resid 54 thr \ ough 56 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 57 or (resid 58 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 59 or (resid 60 through 62 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 65 or (resid 66 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 67 through 68 or (resid 69 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 70 throu \ gh 73 or (resid 89 and (name N or name CA or name C or name O or name CB or name \ HA )) or (resid 90 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 91 or (resid 92 through 93 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 94 through 97 or (r \ esid 98 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 99 or (resid 100 through 101 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 102 or (resid 103 through 106 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 107 or (resid 108 through 111 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or (resid 112 and (name N or name CA or name \ C or name O or name CB or name HA )) or (resid 113 through 114 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 115 or (r \ esid 116 through 120 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 121 through 122 or (resid 123 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 124 or (resid 1 \ 25 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 126 or (resid 127 through 128 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or (resid 136 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or nam \ e HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) \ or resid 137 through 185 or (resid 186 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or (resid 194 and (name N or name CA or nam \ e C or name O or name CB or name HA )) or resid 195 through 269 or (resid 283 an \ d (name N or name CA or name C or name O or name CB or name OG1 or name CG2 or n \ ame HA or name HB or name HG1 or name HG21 or name HG22 or name HG23)) or resid \ 284 through 301 or (resid 302 and (name N or name CA or name C or name O or name \ CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 332 thr \ ough 336 or (resid 359 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD21 \ or name HD22)) or resid 360 through 405 or (resid 410 and (name N or name CA or \ name C or name O or name CB or name OG or name HA or name HB2 or name HB3 or nam \ e HG )) or resid 411 through 440 or (resid 441 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 453 through 531 or (resid \ 532 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 533 or (resid 534 through 535 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 536 through 539 or (resid 540 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 541 through 606 or (resid 607 and (name N or name CA or name C or name O or \ name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 63 \ 7 through 678 or (resid 679 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 680 or (resid 681 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 682 through 696 or r \ esid 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: 1.170 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: 0.870 Extract box with map and model: 1.770 Check model and map are aligned: 0.360 Set scattering table: 0.430 Process input model: 105.350 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.008 0.263 27461 Z= 0.518 Angle : 0.656 12.556 37234 Z= 0.430 Chirality : 0.047 0.253 4294 Planarity : 0.004 0.068 4732 Dihedral : 14.375 167.931 10137 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.53 (0.14), residues: 3416 helix: 0.16 (0.17), residues: 1033 sheet: -1.75 (0.23), residues: 500 loop : -1.48 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 231 HIS 0.006 0.001 HIS L 162 PHE 0.019 0.002 PHE O 534 TYR 0.019 0.002 TYR O 130 ARG 0.007 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue TYR 130 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue TYR 111 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 120 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 540 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue LYS 681 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 3037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 4.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 686 GLN cc_start: 0.8694 (pt0) cc_final: 0.8221 (pm20) REVERT: O 656 HIS cc_start: 0.7110 (m90) cc_final: 0.6777 (m90) REVERT: L 97 GLU cc_start: 0.7582 (tm-30) cc_final: 0.6842 (tm-30) REVERT: L 105 GLU cc_start: 0.6813 (pt0) cc_final: 0.6081 (pt0) REVERT: L 120 ILE cc_start: 0.7021 (mm) cc_final: 0.6773 (mt) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.8595 time to fit residues: 458.4923 Evaluate side-chains 267 residues out of total 3037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 293 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 271 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 165 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 315 optimal weight: 0.9980 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 496 GLN O 655 ASN O 670 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27461 Z= 0.191 Angle : 0.537 5.863 37234 Z= 0.288 Chirality : 0.045 0.165 4294 Planarity : 0.004 0.051 4732 Dihedral : 7.789 174.824 3847 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.52 % Allowed : 5.86 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3416 helix: 0.32 (0.17), residues: 1045 sheet: -1.72 (0.23), residues: 490 loop : -1.39 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 231 HIS 0.010 0.001 HIS A 162 PHE 0.023 0.001 PHE M 104 TYR 0.009 0.001 TYR N 230 ARG 0.005 0.000 ARG N 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue TYR 130 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue TYR 111 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 120 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 540 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue LYS 681 is missing expected H atoms. Skipping. Evaluate side-chains 308 residues out of total 3037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 293 time to evaluate : 4.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 TYR cc_start: 0.7949 (m-80) cc_final: 0.6739 (m-80) REVERT: N 538 MET cc_start: 0.5043 (mpp) cc_final: 0.4645 (mpp) REVERT: L 120 ILE cc_start: 0.7203 (mm) cc_final: 0.6948 (mt) outliers start: 15 outliers final: 12 residues processed: 299 average time/residue: 0.9378 time to fit residues: 442.3908 Evaluate side-chains 283 residues out of total 3037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 271 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 338 ILE Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 330 ASP Chi-restraints excluded: chain L residue 551 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 175 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 315 optimal weight: 4.9990 chunk 341 optimal weight: 7.9990 chunk 281 optimal weight: 9.9990 chunk 313 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27461 Z= 0.306 Angle : 0.548 8.186 37234 Z= 0.292 Chirality : 0.045 0.166 4294 Planarity : 0.004 0.059 4732 Dihedral : 7.786 176.155 3847 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.69 % Allowed : 8.20 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.54 (0.14), residues: 3416 helix: 0.34 (0.17), residues: 1027 sheet: -1.87 (0.23), residues: 499 loop : -1.58 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 231 HIS 0.005 0.001 HIS A 162 PHE 0.018 0.002 PHE M 104 TYR 0.013 0.001 TYR O 593 ARG 0.004 0.000 ARG O 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue TYR 130 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue TYR 111 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 120 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 540 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue LYS 681 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 3037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 4.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 TYR cc_start: 0.8058 (m-80) cc_final: 0.6688 (m-80) REVERT: N 538 MET cc_start: 0.5118 (mpp) cc_final: 0.4706 (mpp) REVERT: O 58 ILE cc_start: 0.8219 (mt) cc_final: 0.7967 (pt) REVERT: O 656 HIS cc_start: 0.7153 (m90) cc_final: 0.6936 (m90) REVERT: L 120 ILE cc_start: 0.7164 (mm) cc_final: 0.6903 (mt) REVERT: L 522 ASP cc_start: 0.7211 (m-30) cc_final: 0.6821 (m-30) outliers start: 20 outliers final: 18 residues processed: 280 average time/residue: 0.9194 time to fit residues: 407.2470 Evaluate side-chains 277 residues out of total 3037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 259 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 277 ASP Chi-restraints excluded: chain O residue 338 ILE Chi-restraints excluded: chain O residue 639 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 330 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 311 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 chunk 316 optimal weight: 0.9980 chunk 335 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 300 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27461 Z= 0.223 Angle : 0.511 7.933 37234 Z= 0.271 Chirality : 0.044 0.163 4294 Planarity : 0.004 0.050 4732 Dihedral : 7.634 178.301 3847 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.72 % Allowed : 9.24 % Favored : 90.04 % 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: -1.45 (0.14), residues: 3416 helix: 0.43 (0.17), residues: 1033 sheet: -1.82 (0.23), residues: 491 loop : -1.53 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 231 HIS 0.006 0.001 HIS N 670 PHE 0.016 0.001 PHE M 104 TYR 0.012 0.001 TYR O 593 ARG 0.004 0.000 ARG N 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue TYR 130 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue TYR 111 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 120 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 540 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue LYS 681 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 3037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 274 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 TYR cc_start: 0.8007 (m-80) cc_final: 0.6576 (m-80) REVERT: M 67 VAL cc_start: 0.5036 (t) cc_final: 0.4823 (m) REVERT: N 538 MET cc_start: 0.5098 (mpp) cc_final: 0.4728 (mpp) REVERT: N 545 ARG cc_start: 0.8253 (mtm180) cc_final: 0.7928 (mtm110) REVERT: O 58 ILE cc_start: 0.8224 (mt) cc_final: 0.8003 (pt) REVERT: L 120 ILE cc_start: 0.7147 (mm) cc_final: 0.6899 (mt) REVERT: L 522 ASP cc_start: 0.7267 (m-30) cc_final: 0.6825 (m-30) outliers start: 21 outliers final: 17 residues processed: 284 average time/residue: 0.9533 time to fit residues: 428.0996 Evaluate side-chains 274 residues out of total 3037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 257 time to evaluate : 4.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 538 MET Chi-restraints excluded: chain D residue 638 ILE Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 260 GLU Chi-restraints excluded: chain O residue 338 ILE Chi-restraints excluded: chain O residue 639 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 330 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 279 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 286 optimal weight: 7.9990 chunk 231 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 301 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 381 ASN O 686 GLN L 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 27461 Z= 0.300 Angle : 0.536 8.642 37234 Z= 0.285 Chirality : 0.045 0.166 4294 Planarity : 0.004 0.053 4732 Dihedral : 7.683 178.516 3847 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.21 % Allowed : 10.23 % Favored : 88.56 % 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: -1.55 (0.14), residues: 3416 helix: 0.43 (0.17), residues: 1027 sheet: -1.94 (0.22), residues: 503 loop : -1.63 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 231 HIS 0.006 0.001 HIS N 670 PHE 0.015 0.002 PHE M 198 TYR 0.012 0.001 TYR A 259 ARG 0.004 0.000 ARG O 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue TYR 130 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue TYR 111 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 120 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 540 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue LYS 681 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 3037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 TYR cc_start: 0.7952 (m-80) cc_final: 0.6611 (m-80) REVERT: N 538 MET cc_start: 0.5131 (mpp) cc_final: 0.4757 (mpp) REVERT: O 58 ILE cc_start: 0.8411 (mt) cc_final: 0.8129 (pt) REVERT: O 686 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.6401 (tp-100) REVERT: L 120 ILE cc_start: 0.7141 (mm) cc_final: 0.6907 (mt) REVERT: L 522 ASP cc_start: 0.7302 (m-30) cc_final: 0.6902 (m-30) outliers start: 35 outliers final: 27 residues processed: 285 average time/residue: 0.9052 time to fit residues: 406.1392 Evaluate side-chains 284 residues out of total 3037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 4.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 538 MET Chi-restraints excluded: chain D residue 638 ILE Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain M residue 503 SER Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 260 GLU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 277 ASP Chi-restraints excluded: chain O residue 338 ILE Chi-restraints excluded: chain O residue 558 LEU Chi-restraints excluded: chain O residue 639 LEU Chi-restraints excluded: chain O residue 686 GLN Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 330 ASP Chi-restraints excluded: chain L residue 508 GLN Chi-restraints excluded: chain L residue 517 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 112 optimal weight: 4.9990 chunk 302 optimal weight: 0.0770 chunk 66 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 335 optimal weight: 0.5980 chunk 278 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 overall best weight: 2.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27461 Z= 0.225 Angle : 0.510 9.173 37234 Z= 0.270 Chirality : 0.044 0.163 4294 Planarity : 0.004 0.051 4732 Dihedral : 7.606 179.324 3847 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.93 % Allowed : 11.13 % Favored : 87.94 % 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: -1.45 (0.14), residues: 3416 helix: 0.51 (0.17), residues: 1027 sheet: -1.84 (0.23), residues: 497 loop : -1.57 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 231 HIS 0.006 0.001 HIS N 162 PHE 0.014 0.001 PHE M 104 TYR 0.012 0.001 TYR A 259 ARG 0.003 0.000 ARG N 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6832 Ramachandran restraints generated. 3416 Oldfield, 0 Emsley, 3416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue TYR 130 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue VAL 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue TYR 60 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue TYR 111 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 120 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 540 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue TYR 305 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue TYR 643 is missing expected H atoms. Skipping. Residue LYS 681 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 3037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 4.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 TYR cc_start: 0.7955 (m-80) cc_final: 0.6617 (m-80) REVERT: N 237 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6844 (mt-10) REVERT: N 479 LYS cc_start: 0.7406 (tmtt) cc_final: 0.6902 (mmmt) REVERT: N 538 MET cc_start: 0.5119 (mpp) cc_final: 0.4733 (mpp) REVERT: O 58 ILE cc_start: 0.8408 (mt) cc_final: 0.8142 (pt) REVERT: O 686 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7572 (mm110) REVERT: L 120 ILE cc_start: 0.7083 (mm) cc_final: 0.6854 (mt) REVERT: L 522 ASP cc_start: 0.7285 (m-30) cc_final: 0.6905 (m-30) outliers start: 27 outliers final: 22 residues processed: 285 average time/residue: 0.9361 time to fit residues: 422.1014 Evaluate side-chains 276 residues out of total 3037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 253 time to evaluate : 4.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 538 MET Chi-restraints excluded: chain D residue 638 ILE Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 503 SER Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 260 GLU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 338 ILE Chi-restraints excluded: chain O residue 639 LEU Chi-restraints excluded: chain O residue 686 GLN Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 330 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 323 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 245 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 334 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 381 ASN L 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1482 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: