Starting phenix.real_space_refine on Sat Sep 12 20:20:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pk4_20354/09_2026/6pk4_20354.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pk4_20354/09_2026/6pk4_20354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pk4_20354/09_2026/6pk4_20354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pk4_20354/09_2026/6pk4_20354.map" model { file = "/net/cci-nas-00/data/ceres_data/6pk4_20354/09_2026/6pk4_20354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pk4_20354/09_2026/6pk4_20354.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pk4_20354/09_2026/6pk4_20354.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pk4_20354/09_2026/6pk4_20354.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.023 sd= 0.773 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 96 5.16 5 C 11332 2.51 5 N 3084 2.21 5 O 3340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17876 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4409 Classifications: {'peptide': 559} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 528} Chain: "B" Number of atoms: 4409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4409 Classifications: {'peptide': 559} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 528} Chain: "C" Number of atoms: 4409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4409 Classifications: {'peptide': 559} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 528} Chain: "D" Number of atoms: 4409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4409 Classifications: {'peptide': 559} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 528} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU A 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU A 155 " occ=0.75 residue: pdb=" N CYS A 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS A 243 " occ=0.75 residue: pdb=" N GLU B 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU B 155 " occ=0.75 residue: pdb=" N CYS B 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS B 243 " occ=0.75 residue: pdb=" N GLU C 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU C 155 " occ=0.75 residue: pdb=" N CYS C 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS C 243 " occ=0.75 residue: pdb=" N GLU D 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU D 155 " occ=0.75 residue: pdb=" N CYS D 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS D 243 " occ=0.75 Time building chain proxies: 2.96, per 1000 atoms: 0.17 Number of scatterers: 17876 At special positions: 0 Unit cell: (137.55, 87.15, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 24 15.00 O 3340 8.00 N 3084 7.00 C 11332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 693.9 milliseconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4120 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 28 sheets defined 42.9% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 15 through 31 removed outlier: 3.606A pdb=" N SER A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.778A pdb=" N THR A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 79 removed outlier: 3.742A pdb=" N ASN A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.502A pdb=" N ASN A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 4.044A pdb=" N MET A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 removed outlier: 3.572A pdb=" N VAL A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 162 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.023A pdb=" N VAL A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.791A pdb=" N PHE A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.656A pdb=" N ASP A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 328 removed outlier: 4.356A pdb=" N ALA A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 343 through 350 removed outlier: 4.061A pdb=" N GLU A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 removed outlier: 3.776A pdb=" N PHE A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 391 removed outlier: 4.781A pdb=" N GLN A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.619A pdb=" N VAL A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.947A pdb=" N LYS A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 removed outlier: 3.592A pdb=" N ILE A 489 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 493 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 548 removed outlier: 3.615A pdb=" N GLY A 542 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 558 removed outlier: 3.674A pdb=" N LEU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 558 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 31 removed outlier: 3.607A pdb=" N SER B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.778A pdb=" N THR B 49 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 removed outlier: 3.742A pdb=" N ASN B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.502A pdb=" N ASN B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 removed outlier: 4.044A pdb=" N MET B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 170 removed outlier: 3.572A pdb=" N VAL B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 162 " --> pdb=" O PRO B 158 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 223 through 234 Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.023A pdb=" N VAL B 255 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 270 removed outlier: 3.792A pdb=" N PHE B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.656A pdb=" N ASP B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 328 removed outlier: 4.357A pdb=" N ALA B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 324 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 343 through 350 removed outlier: 4.062A pdb=" N GLU B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.776A pdb=" N PHE B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 363 " --> pdb=" O GLN B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 391 removed outlier: 4.781A pdb=" N GLN B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 413 removed outlier: 3.619A pdb=" N VAL B 406 " --> pdb=" O MET B 402 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.947A pdb=" N LYS B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 removed outlier: 3.592A pdb=" N ILE B 489 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 491 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU B 493 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 548 removed outlier: 3.615A pdb=" N GLY B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.674A pdb=" N LEU B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 558 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 31 removed outlier: 3.606A pdb=" N SER C 22 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 50 removed outlier: 3.778A pdb=" N THR C 49 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 79 removed outlier: 3.742A pdb=" N ASN C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.501A pdb=" N ASN C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 131 removed outlier: 4.044A pdb=" N MET C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 170 removed outlier: 3.572A pdb=" N VAL C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 161 " --> pdb=" O MET C 157 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 166 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 223 through 234 Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.022A pdb=" N VAL C 255 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 270 removed outlier: 3.791A pdb=" N PHE C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 267 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 removed outlier: 3.656A pdb=" N ASP C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 292 " --> pdb=" O MET C 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 328 removed outlier: 4.357A pdb=" N ALA C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 324 " --> pdb=" O ALA C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 343 through 350 removed outlier: 4.061A pdb=" N GLU C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 removed outlier: 3.777A pdb=" N PHE C 354 " --> pdb=" O ASP C 350 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU C 356 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 363 " --> pdb=" O GLN C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 391 removed outlier: 4.781A pdb=" N GLN C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 413 removed outlier: 3.619A pdb=" N VAL C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 410 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 469 removed outlier: 3.947A pdb=" N LYS C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 467 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 493 removed outlier: 3.592A pdb=" N ILE C 489 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 491 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU C 493 " --> pdb=" O LYS C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 548 removed outlier: 3.614A pdb=" N GLY C 542 " --> pdb=" O PRO C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.674A pdb=" N LEU C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 31 removed outlier: 3.606A pdb=" N SER D 22 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 50 removed outlier: 3.778A pdb=" N THR D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 79 removed outlier: 3.742A pdb=" N ASN D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 90 through 99 removed outlier: 3.501A pdb=" N ASN D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 131 removed outlier: 4.045A pdb=" N MET D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.571A pdb=" N VAL D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 162 " --> pdb=" O PRO D 158 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 223 through 234 Processing helix chain 'D' and resid 251 through 260 removed outlier: 4.023A pdb=" N VAL D 255 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU D 258 " --> pdb=" O PRO D 254 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 270 removed outlier: 3.791A pdb=" N PHE D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 removed outlier: 3.656A pdb=" N ASP D 290 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 292 " --> pdb=" O MET D 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 328 removed outlier: 4.357A pdb=" N ALA D 320 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 343 through 350 removed outlier: 4.061A pdb=" N GLU D 347 " --> pdb=" O GLU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 363 removed outlier: 3.777A pdb=" N PHE D 354 " --> pdb=" O ASP D 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU D 356 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 363 " --> pdb=" O GLN D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 391 removed outlier: 4.780A pdb=" N GLN D 383 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER D 386 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.619A pdb=" N VAL D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 410 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.948A pdb=" N LYS D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 467 " --> pdb=" O ILE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 493 removed outlier: 3.593A pdb=" N ILE D 489 " --> pdb=" O PRO D 486 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN D 491 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU D 493 " --> pdb=" O LYS D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 548 removed outlier: 3.614A pdb=" N GLY D 542 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 558 removed outlier: 3.674A pdb=" N LEU D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 558 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 7.106A pdb=" N LYS A 2 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE A 145 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE A 4 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 147 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 6 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR A 3 " --> pdb=" O CYS A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 182 removed outlier: 6.269A pdb=" N SER A 181 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 214 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE A 244 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N CYS A 216 " --> pdb=" O ILE A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 305 removed outlier: 6.564A pdb=" N LEU A 303 " --> pdb=" O ILE A 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 369 removed outlier: 7.215A pdb=" N ILE A 367 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N VAL A 398 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 369 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE A 395 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL A 523 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLY A 397 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE A 520 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 522 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 513 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 419 through 421 removed outlier: 3.501A pdb=" N ASP A 420 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 438 through 440 removed outlier: 5.903A pdb=" N GLU A 438 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY A 445 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 440 " --> pdb=" O ASN A 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 477 Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 removed outlier: 7.106A pdb=" N LYS B 2 " --> pdb=" O CYS B 143 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE B 145 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE B 4 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 147 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 6 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR B 3 " --> pdb=" O CYS B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 180 through 182 removed outlier: 6.268A pdb=" N SER B 181 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 214 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE B 244 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N CYS B 216 " --> pdb=" O ILE B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 303 through 305 removed outlier: 6.564A pdb=" N LEU B 303 " --> pdb=" O ILE B 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 367 through 369 removed outlier: 7.215A pdb=" N ILE B 367 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N VAL B 398 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 369 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE B 395 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL B 523 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLY B 397 " --> pdb=" O VAL B 523 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE B 520 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 522 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 513 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 419 through 421 removed outlier: 3.501A pdb=" N ASP B 420 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 438 through 440 removed outlier: 5.904A pdb=" N GLU B 438 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY B 445 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 440 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 473 through 477 Processing sheet with id=AB6, first strand: chain 'C' and resid 87 through 89 removed outlier: 7.106A pdb=" N LYS C 2 " --> pdb=" O CYS C 143 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE C 145 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE C 4 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU C 147 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL C 6 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 180 through 182 removed outlier: 6.269A pdb=" N SER C 181 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 214 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE C 244 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N CYS C 216 " --> pdb=" O ILE C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 303 through 305 removed outlier: 6.564A pdb=" N LEU C 303 " --> pdb=" O ILE C 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 367 through 369 removed outlier: 7.215A pdb=" N ILE C 367 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N VAL C 398 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 369 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE C 395 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL C 523 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLY C 397 " --> pdb=" O VAL C 523 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE C 520 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 522 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 513 " --> pdb=" O SER C 498 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 419 through 421 removed outlier: 3.501A pdb=" N ASP C 420 " --> pdb=" O VAL C 430 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 438 through 440 removed outlier: 5.904A pdb=" N GLU C 438 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY C 445 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN C 440 " --> pdb=" O ASN C 443 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 473 through 477 Processing sheet with id=AC4, first strand: chain 'D' and resid 87 through 89 removed outlier: 7.105A pdb=" N LYS D 2 " --> pdb=" O CYS D 143 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE D 145 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE D 4 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU D 147 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL D 6 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR D 3 " --> pdb=" O CYS D 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 180 through 182 removed outlier: 6.268A pdb=" N SER D 181 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE D 214 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE D 244 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N CYS D 216 " --> pdb=" O ILE D 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 303 through 305 removed outlier: 6.563A pdb=" N LEU D 303 " --> pdb=" O ILE D 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 367 through 369 removed outlier: 7.215A pdb=" N ILE D 367 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N VAL D 398 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL D 369 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE D 395 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL D 523 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLY D 397 " --> pdb=" O VAL D 523 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE D 520 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 522 " --> pdb=" O ILE D 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 513 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 419 through 421 removed outlier: 3.501A pdb=" N ASP D 420 " --> pdb=" O VAL D 430 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 438 through 440 removed outlier: 5.904A pdb=" N GLU D 438 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY D 445 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN D 440 " --> pdb=" O ASN D 443 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 473 through 477 488 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 2726 1.25 - 1.39: 4536 1.39 - 1.53: 10173 1.53 - 1.68: 673 1.68 - 1.82: 152 Bond restraints: 18260 Sorted by residual: bond pdb=" C2' UTP A 601 " pdb=" C3' UTP A 601 " ideal model delta sigma weight residual 1.533 1.355 0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C2' UTP B 601 " pdb=" C3' UTP B 601 " ideal model delta sigma weight residual 1.533 1.355 0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C2' UTP C 601 " pdb=" C3' UTP C 601 " ideal model delta sigma weight residual 1.533 1.356 0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" C2' UTP D 601 " pdb=" C3' UTP D 601 " ideal model delta sigma weight residual 1.533 1.356 0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.51e+01 ... (remaining 18255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 24088 3.86 - 7.73: 560 7.73 - 11.59: 84 11.59 - 15.46: 16 15.46 - 19.32: 12 Bond angle restraints: 24760 Sorted by residual: angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 120.55 19.32 1.00e+00 1.00e+00 3.73e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 120.58 19.29 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 120.60 19.27 1.00e+00 1.00e+00 3.71e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 120.61 19.26 1.00e+00 1.00e+00 3.71e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 120.57 16.26 1.00e+00 1.00e+00 2.64e+02 ... (remaining 24755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.49: 9930 13.49 - 26.99: 763 26.99 - 40.48: 277 40.48 - 53.98: 74 53.98 - 67.47: 24 Dihedral angle restraints: 11068 sinusoidal: 4648 harmonic: 6420 Sorted by residual: dihedral pdb=" CA VAL B 58 " pdb=" C VAL B 58 " pdb=" N PHE B 59 " pdb=" CA PHE B 59 " ideal model delta harmonic sigma weight residual 180.00 136.26 43.74 0 5.00e+00 4.00e-02 7.65e+01 dihedral pdb=" CA VAL C 58 " pdb=" C VAL C 58 " pdb=" N PHE C 59 " pdb=" CA PHE C 59 " ideal model delta harmonic sigma weight residual 180.00 136.29 43.71 0 5.00e+00 4.00e-02 7.64e+01 dihedral pdb=" CA VAL D 58 " pdb=" C VAL D 58 " pdb=" N PHE D 59 " pdb=" CA PHE D 59 " ideal model delta harmonic sigma weight residual 180.00 136.31 43.69 0 5.00e+00 4.00e-02 7.64e+01 ... (remaining 11065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2583 0.137 - 0.274: 125 0.274 - 0.411: 28 0.411 - 0.548: 8 0.548 - 0.685: 8 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CB ILE B 301 " pdb=" CA ILE B 301 " pdb=" CG1 ILE B 301 " pdb=" CG2 ILE B 301 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CB ILE D 301 " pdb=" CA ILE D 301 " pdb=" CG1 ILE D 301 " pdb=" CG2 ILE D 301 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CB ILE A 301 " pdb=" CA ILE A 301 " pdb=" CG1 ILE A 301 " pdb=" CG2 ILE A 301 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 2749 not shown) Planarity restraints: 3176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 66 " 0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C GLU A 66 " -0.088 2.00e-02 2.50e+03 pdb=" O GLU A 66 " 0.034 2.00e-02 2.50e+03 pdb=" N VAL A 67 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 66 " -0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C GLU D 66 " 0.088 2.00e-02 2.50e+03 pdb=" O GLU D 66 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL D 67 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 66 " -0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C GLU C 66 " 0.088 2.00e-02 2.50e+03 pdb=" O GLU C 66 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL C 67 " -0.029 2.00e-02 2.50e+03 ... (remaining 3173 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 40 2.08 - 2.79: 4505 2.79 - 3.49: 23287 3.49 - 4.20: 41822 4.20 - 4.90: 71275 Nonbonded interactions: 140929 Sorted by model distance: nonbonded pdb=" O LEU B 69 " pdb=" N LEU B 71 " model vdw 1.380 3.120 nonbonded pdb=" O LEU A 69 " pdb=" N LEU A 71 " model vdw 1.381 3.120 nonbonded pdb=" O LEU D 69 " pdb=" N LEU D 71 " model vdw 1.381 3.120 nonbonded pdb=" O LEU C 69 " pdb=" N LEU C 71 " model vdw 1.381 3.120 nonbonded pdb=" OD1 ASP A 70 " pdb=" O1B ATP A 602 " model vdw 1.413 3.040 ... (remaining 140924 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.720 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.010 0.178 18264 Z= 0.557 Angle : 1.440 19.319 24760 Z= 0.830 Chirality : 0.086 0.685 2752 Planarity : 0.009 0.072 3176 Dihedral : 12.195 67.470 6948 Min Nonbonded Distance : 1.380 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.54 % Favored : 91.56 % Rotamer: Outliers : 1.44 % Allowed : 5.35 % Favored : 93.21 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 1.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.81 (0.14), residues: 2228 helix: -3.89 (0.11), residues: 768 sheet: -3.32 (0.22), residues: 380 loop : -2.47 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 465 TYR 0.058 0.005 TYR B 94 PHE 0.033 0.003 PHE A 482 TRP 0.018 0.003 TRP A 124 HIS 0.007 0.002 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.01011 / 0.54 (18260) covalent geometry : angle 1.44020 / 0.83 (24760) hydrogen bonds : bond 0.31292 / 21.13 ( 488) hydrogen bonds : angle 9.74253 / 6.68 ( 1416) Misc. bond : bond 0.09197 / 4.61 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 492 time to evaluate : 0.697 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: symmetry clash revert: symmetry clash REVERT: A 12 SER cc_start: 0.8461 (p) cc_final: 0.8160 (p) REVERT: A 122 GLN cc_start: 0.8238 (pt0) cc_final: 0.7859 (pp30) REVERT: A 139 GLU cc_start: 0.8098 (tt0) cc_final: 0.7109 (mp0) REVERT: A 186 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5886 (mm) REVERT: A 335 MET cc_start: 0.7627 (ptp) cc_final: 0.7104 (ptp) REVERT: B 12 SER cc_start: 0.8459 (p) cc_final: 0.8158 (p) REVERT: B 122 GLN cc_start: 0.8237 (pt0) cc_final: 0.7859 (pp30) REVERT: B 139 GLU cc_start: 0.8089 (tt0) cc_final: 0.7095 (mp0) REVERT: B 186 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5886 (mm) REVERT: B 335 MET cc_start: 0.7631 (ptp) cc_final: 0.7109 (ptp) REVERT: C 122 GLN cc_start: 0.8255 (pt0) cc_final: 0.7859 (pp30) REVERT: C 139 GLU cc_start: 0.8135 (tt0) cc_final: 0.7197 (mp0) REVERT: C 186 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5880 (mm) REVERT: C 322 GLU cc_start: 0.8246 (pt0) cc_final: 0.7891 (pt0) REVERT: C 335 MET cc_start: 0.7651 (ptp) cc_final: 0.7118 (ptp) REVERT: D 122 GLN cc_start: 0.8252 (pt0) cc_final: 0.7858 (pp30) REVERT: D 139 GLU cc_start: 0.8136 (tt0) cc_final: 0.7198 (mp0) REVERT: D 186 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5863 (mm) REVERT: D 322 GLU cc_start: 0.8241 (pt0) cc_final: 0.7904 (pt0) REVERT: D 335 MET cc_start: 0.7648 (ptp) cc_final: 0.7111 (ptp) outliers start: 28 outliers final: 20 residues processed: 516 average time/residue: 0.1402 time to fit residues: 106.9345 Evaluate side-chains 260 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 313 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN A 99 ASN A 192 GLN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN B 99 ASN B 192 GLN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN C 99 ASN C 192 GLN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 99 ASN D 192 GLN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.121107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097390 restraints weight = 39508.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101207 restraints weight = 19869.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103838 restraints weight = 12707.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.105632 restraints weight = 9321.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106925 restraints weight = 7471.001| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18264 Z= 0.203 Angle : 0.819 9.357 24760 Z= 0.418 Chirality : 0.056 0.648 2752 Planarity : 0.007 0.059 3176 Dihedral : 10.969 59.435 2616 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.91 % Favored : 92.82 % Rotamer: Outliers : 4.78 % Allowed : 12.19 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.80 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.16), residues: 2228 helix: -2.51 (0.14), residues: 820 sheet: -2.74 (0.24), residues: 368 loop : -1.94 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 202 TYR 0.019 0.002 TYR D 53 PHE 0.016 0.002 PHE A 482 TRP 0.022 0.002 TRP C 124 HIS 0.004 0.001 HIS B 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (18260) covalent geometry : angle 0.81924 / 0.42 (24760) hydrogen bonds : bond 0.04595 / 3.09 ( 488) hydrogen bonds : angle 5.56773 / 3.89 ( 1416) Misc. bond : bond 0.00263 / 0.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 274 time to evaluate : 0.577 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: A 2 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8285 (mmmt) REVERT: A 16 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7706 (mtmt) REVERT: A 122 GLN cc_start: 0.8212 (pt0) cc_final: 0.7852 (pp30) REVERT: A 139 GLU cc_start: 0.8089 (tt0) cc_final: 0.7103 (mp0) REVERT: A 157 MET cc_start: 0.8538 (mmm) cc_final: 0.7744 (mmm) REVERT: A 212 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8040 (t0) REVERT: A 301 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7436 (mp) REVERT: A 335 MET cc_start: 0.7590 (ptp) cc_final: 0.6963 (ptp) REVERT: A 362 CYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7280 (p) REVERT: A 496 ASP cc_start: 0.7424 (p0) cc_final: 0.6844 (p0) REVERT: B 2 LYS cc_start: 0.8504 (mmtm) cc_final: 0.8289 (mmmt) REVERT: B 16 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7711 (mtmt) REVERT: B 122 GLN cc_start: 0.8212 (pt0) cc_final: 0.7850 (pp30) REVERT: B 139 GLU cc_start: 0.8099 (tt0) cc_final: 0.7109 (mp0) REVERT: B 157 MET cc_start: 0.8537 (mmm) cc_final: 0.7741 (mmm) REVERT: B 212 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8043 (t0) REVERT: B 301 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7399 (mp) REVERT: B 335 MET cc_start: 0.7601 (ptp) cc_final: 0.6969 (ptp) REVERT: B 362 CYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7277 (p) REVERT: B 496 ASP cc_start: 0.7414 (p0) cc_final: 0.6840 (p0) REVERT: C 2 LYS cc_start: 0.8510 (mmtm) cc_final: 0.8284 (mmmt) REVERT: C 16 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7705 (mtmt) REVERT: C 122 GLN cc_start: 0.8239 (pt0) cc_final: 0.7859 (pp30) REVERT: C 139 GLU cc_start: 0.8109 (tt0) cc_final: 0.7138 (mp0) REVERT: C 157 MET cc_start: 0.8536 (mmm) cc_final: 0.7730 (mmm) REVERT: C 191 GLU cc_start: 0.7687 (mp0) cc_final: 0.7438 (mp0) REVERT: C 209 LEU cc_start: 0.9013 (mp) cc_final: 0.8691 (mm) REVERT: C 212 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8118 (t0) REVERT: C 301 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7427 (mp) REVERT: C 335 MET cc_start: 0.7558 (ptp) cc_final: 0.6980 (ptp) REVERT: C 496 ASP cc_start: 0.7336 (p0) cc_final: 0.6461 (p0) REVERT: D 2 LYS cc_start: 0.8489 (mmtm) cc_final: 0.8275 (mmmt) REVERT: D 16 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7708 (mtmt) REVERT: D 122 GLN cc_start: 0.8240 (pt0) cc_final: 0.7861 (pp30) REVERT: D 139 GLU cc_start: 0.8097 (tt0) cc_final: 0.7138 (mp0) REVERT: D 157 MET cc_start: 0.8529 (mmm) cc_final: 0.7726 (mmm) REVERT: D 191 GLU cc_start: 0.7572 (mp0) cc_final: 0.7357 (mp0) REVERT: D 209 LEU cc_start: 0.9006 (mp) cc_final: 0.8687 (mm) REVERT: D 212 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8114 (t0) REVERT: D 301 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7409 (mp) REVERT: D 335 MET cc_start: 0.7539 (ptp) cc_final: 0.6963 (ptp) REVERT: D 496 ASP cc_start: 0.7349 (p0) cc_final: 0.6535 (p0) outliers start: 93 outliers final: 28 residues processed: 337 average time/residue: 0.1219 time to fit residues: 63.9325 Evaluate side-chains 257 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 521 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 117 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 209 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.121632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097074 restraints weight = 40081.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100821 restraints weight = 20404.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.103388 restraints weight = 13124.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.105167 restraints weight = 9699.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106408 restraints weight = 7847.011| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18264 Z= 0.188 Angle : 0.732 8.790 24760 Z= 0.371 Chirality : 0.053 0.622 2752 Planarity : 0.005 0.058 3176 Dihedral : 9.707 59.638 2584 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.05 % Favored : 92.77 % Rotamer: Outliers : 4.73 % Allowed : 13.94 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.16), residues: 2228 helix: -1.55 (0.16), residues: 856 sheet: -2.59 (0.25), residues: 356 loop : -1.81 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 76 TYR 0.015 0.002 TYR B 106 PHE 0.017 0.002 PHE C 159 TRP 0.016 0.002 TRP C 124 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (18260) covalent geometry : angle 0.73160 / 0.37 (24760) hydrogen bonds : bond 0.04038 / 2.74 ( 488) hydrogen bonds : angle 5.00887 / 3.51 ( 1416) Misc. bond : bond 0.00052 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 232 time to evaluate : 0.721 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8283 (mmmt) REVERT: A 122 GLN cc_start: 0.8252 (pt0) cc_final: 0.7885 (pp30) REVERT: A 139 GLU cc_start: 0.8100 (tt0) cc_final: 0.7098 (mp0) REVERT: A 191 GLU cc_start: 0.7579 (mp0) cc_final: 0.7373 (mp0) REVERT: A 212 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8057 (t0) REVERT: A 335 MET cc_start: 0.7576 (ptp) cc_final: 0.6927 (ptp) REVERT: A 362 CYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7353 (p) REVERT: B 2 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8283 (mmmt) REVERT: B 122 GLN cc_start: 0.8253 (pt0) cc_final: 0.7884 (pp30) REVERT: B 139 GLU cc_start: 0.8111 (tt0) cc_final: 0.7101 (mp0) REVERT: B 191 GLU cc_start: 0.7569 (mp0) cc_final: 0.7363 (mp0) REVERT: B 212 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8059 (t0) REVERT: B 335 MET cc_start: 0.7600 (ptp) cc_final: 0.6928 (ptp) REVERT: B 362 CYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7345 (p) REVERT: C 2 LYS cc_start: 0.8644 (mmtm) cc_final: 0.8348 (mmmt) REVERT: C 122 GLN cc_start: 0.8271 (pt0) cc_final: 0.7890 (pp30) REVERT: C 139 GLU cc_start: 0.8130 (tt0) cc_final: 0.7129 (mp0) REVERT: C 142 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8899 (tt) REVERT: C 191 GLU cc_start: 0.7840 (mp0) cc_final: 0.7552 (mp0) REVERT: C 335 MET cc_start: 0.7534 (ptp) cc_final: 0.6879 (ptp) REVERT: C 496 ASP cc_start: 0.7130 (p0) cc_final: 0.6505 (p0) REVERT: D 2 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8319 (mmmt) REVERT: D 122 GLN cc_start: 0.8272 (pt0) cc_final: 0.7886 (pp30) REVERT: D 139 GLU cc_start: 0.8133 (tt0) cc_final: 0.7149 (mp0) REVERT: D 191 GLU cc_start: 0.7574 (mp0) cc_final: 0.7338 (mp0) REVERT: D 212 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8077 (t0) REVERT: D 301 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7217 (mp) REVERT: D 335 MET cc_start: 0.7520 (ptp) cc_final: 0.6857 (ptp) REVERT: D 409 PHE cc_start: 0.7820 (t80) cc_final: 0.7604 (t80) REVERT: D 496 ASP cc_start: 0.7160 (p0) cc_final: 0.6491 (p0) outliers start: 92 outliers final: 42 residues processed: 300 average time/residue: 0.1344 time to fit residues: 62.7960 Evaluate side-chains 257 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS A 167 GLN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS B 167 GLN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN C 192 GLN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.122971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.098510 restraints weight = 39596.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.102276 restraints weight = 20157.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.104824 restraints weight = 12957.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106612 restraints weight = 9605.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.107868 restraints weight = 7768.338| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18264 Z= 0.137 Angle : 0.688 9.032 24760 Z= 0.343 Chirality : 0.051 0.567 2752 Planarity : 0.005 0.057 3176 Dihedral : 9.129 59.926 2584 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.48 % Favored : 94.34 % Rotamer: Outliers : 4.01 % Allowed : 16.20 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.17), residues: 2228 helix: -1.01 (0.17), residues: 856 sheet: -2.80 (0.24), residues: 356 loop : -1.68 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 202 TYR 0.013 0.002 TYR C 42 PHE 0.018 0.001 PHE B 159 TRP 0.013 0.002 TRP C 124 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (18260) covalent geometry : angle 0.68757 / 0.34 (24760) hydrogen bonds : bond 0.03368 / 2.26 ( 488) hydrogen bonds : angle 4.64450 / 3.25 ( 1416) Misc. bond : bond 0.00036 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 240 time to evaluate : 0.716 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: A 54 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 122 GLN cc_start: 0.8202 (pt0) cc_final: 0.7882 (pp30) REVERT: A 139 GLU cc_start: 0.8157 (tt0) cc_final: 0.7075 (mp0) REVERT: A 157 MET cc_start: 0.8581 (mmm) cc_final: 0.7721 (mmm) REVERT: A 191 GLU cc_start: 0.7578 (mp0) cc_final: 0.7370 (mp0) REVERT: A 335 MET cc_start: 0.7555 (ptp) cc_final: 0.6860 (ptp) REVERT: A 362 CYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7269 (p) REVERT: B 54 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 75 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 122 GLN cc_start: 0.8180 (pt0) cc_final: 0.7861 (pp30) REVERT: B 139 GLU cc_start: 0.8153 (tt0) cc_final: 0.7075 (mp0) REVERT: B 157 MET cc_start: 0.8573 (mmm) cc_final: 0.7728 (mmm) REVERT: B 191 GLU cc_start: 0.7568 (mp0) cc_final: 0.7252 (mp0) REVERT: B 335 MET cc_start: 0.7556 (ptp) cc_final: 0.6856 (ptp) REVERT: B 362 CYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7262 (p) REVERT: C 2 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8171 (mmmt) REVERT: C 54 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7319 (tm-30) REVERT: C 75 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8084 (tm-30) REVERT: C 122 GLN cc_start: 0.8239 (pt0) cc_final: 0.7885 (pp30) REVERT: C 139 GLU cc_start: 0.8193 (tt0) cc_final: 0.6969 (mp0) REVERT: C 191 GLU cc_start: 0.7920 (mp0) cc_final: 0.7663 (mp0) REVERT: C 335 MET cc_start: 0.7595 (ptp) cc_final: 0.6884 (ptp) REVERT: C 496 ASP cc_start: 0.7661 (p0) cc_final: 0.7153 (p0) REVERT: D 54 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7333 (tm-30) REVERT: D 122 GLN cc_start: 0.8241 (pt0) cc_final: 0.7878 (pp30) REVERT: D 139 GLU cc_start: 0.8178 (tt0) cc_final: 0.7134 (mp0) REVERT: D 335 MET cc_start: 0.7585 (ptp) cc_final: 0.6875 (ptp) REVERT: D 409 PHE cc_start: 0.7755 (t80) cc_final: 0.7518 (t80) REVERT: D 496 ASP cc_start: 0.7510 (p0) cc_final: 0.6906 (p0) outliers start: 78 outliers final: 45 residues processed: 304 average time/residue: 0.1300 time to fit residues: 62.3257 Evaluate side-chains 260 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 91 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 188 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 165 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS C 237 ASN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS D 167 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.122081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097105 restraints weight = 39804.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.100886 restraints weight = 20867.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.103451 restraints weight = 13627.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.105230 restraints weight = 10145.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106450 restraints weight = 8243.579| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18264 Z= 0.172 Angle : 0.700 10.460 24760 Z= 0.348 Chirality : 0.048 0.275 2752 Planarity : 0.005 0.056 3176 Dihedral : 8.867 59.995 2580 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.06 % Favored : 93.76 % Rotamer: Outliers : 4.22 % Allowed : 17.39 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.17), residues: 2228 helix: -0.67 (0.17), residues: 852 sheet: -2.75 (0.25), residues: 364 loop : -1.58 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 202 TYR 0.014 0.002 TYR A 468 PHE 0.015 0.002 PHE A 520 TRP 0.013 0.002 TRP C 124 HIS 0.007 0.001 HIS C 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (18260) covalent geometry : angle 0.69964 / 0.35 (24760) hydrogen bonds : bond 0.03377 / 2.30 ( 488) hydrogen bonds : angle 4.59300 / 3.22 ( 1416) Misc. bond : bond 0.00057 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 229 time to evaluate : 0.702 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: A 122 GLN cc_start: 0.8265 (pt0) cc_final: 0.7880 (pp30) REVERT: A 139 GLU cc_start: 0.8201 (tt0) cc_final: 0.7141 (mp0) REVERT: A 191 GLU cc_start: 0.7671 (mp0) cc_final: 0.7441 (mp0) REVERT: A 335 MET cc_start: 0.7591 (ptp) cc_final: 0.6872 (ptp) REVERT: A 362 CYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7367 (p) REVERT: A 396 LEU cc_start: 0.9261 (tp) cc_final: 0.9040 (tt) REVERT: A 402 MET cc_start: 0.7893 (ttt) cc_final: 0.7505 (ttt) REVERT: A 409 PHE cc_start: 0.8125 (t80) cc_final: 0.7694 (t80) REVERT: B 122 GLN cc_start: 0.8268 (pt0) cc_final: 0.7883 (pp30) REVERT: B 139 GLU cc_start: 0.8204 (tt0) cc_final: 0.7142 (mp0) REVERT: B 191 GLU cc_start: 0.7647 (mp0) cc_final: 0.7403 (mp0) REVERT: B 335 MET cc_start: 0.7612 (ptp) cc_final: 0.6923 (ptp) REVERT: B 362 CYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7330 (p) REVERT: B 396 LEU cc_start: 0.9254 (tp) cc_final: 0.9026 (tt) REVERT: B 402 MET cc_start: 0.7932 (ttt) cc_final: 0.7472 (ttt) REVERT: B 409 PHE cc_start: 0.8183 (t80) cc_final: 0.7735 (t80) REVERT: C 2 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8150 (mmmt) REVERT: C 75 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7996 (tm-30) REVERT: C 122 GLN cc_start: 0.8340 (pt0) cc_final: 0.7943 (pp30) REVERT: C 157 MET cc_start: 0.8563 (mmm) cc_final: 0.7717 (mmm) REVERT: C 191 GLU cc_start: 0.7892 (mp0) cc_final: 0.7636 (mp0) REVERT: C 335 MET cc_start: 0.7531 (ptp) cc_final: 0.6666 (ptp) REVERT: C 496 ASP cc_start: 0.7700 (p0) cc_final: 0.7237 (p0) REVERT: D 122 GLN cc_start: 0.8348 (pt0) cc_final: 0.7942 (pp30) REVERT: D 139 GLU cc_start: 0.8209 (tt0) cc_final: 0.7146 (mp0) REVERT: D 157 MET cc_start: 0.8568 (mmm) cc_final: 0.7716 (mmm) REVERT: D 335 MET cc_start: 0.7527 (ptp) cc_final: 0.6663 (ptp) REVERT: D 409 PHE cc_start: 0.8023 (t80) cc_final: 0.7747 (t80) REVERT: D 496 ASP cc_start: 0.7758 (p0) cc_final: 0.7238 (p0) REVERT: D 509 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6513 (mmp) outliers start: 82 outliers final: 59 residues processed: 295 average time/residue: 0.1258 time to fit residues: 58.9961 Evaluate side-chains 271 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 15 optimal weight: 0.0030 chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 101 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 HIS ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS ** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.123110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098469 restraints weight = 39070.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.102244 restraints weight = 20249.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104878 restraints weight = 13151.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.106700 restraints weight = 9762.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.107997 restraints weight = 7893.413| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18264 Z= 0.124 Angle : 0.670 10.893 24760 Z= 0.331 Chirality : 0.047 0.205 2752 Planarity : 0.005 0.057 3176 Dihedral : 8.599 59.987 2580 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.60 % Allowed : 19.24 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.17), residues: 2228 helix: -0.54 (0.18), residues: 848 sheet: -2.71 (0.25), residues: 364 loop : -1.49 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 389 TYR 0.012 0.002 TYR C 42 PHE 0.013 0.001 PHE B 159 TRP 0.011 0.001 TRP C 124 HIS 0.005 0.001 HIS C 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (18260) covalent geometry : angle 0.67029 / 0.33 (24760) hydrogen bonds : bond 0.03034 / 2.07 ( 488) hydrogen bonds : angle 4.38668 / 3.07 ( 1416) Misc. bond : bond 0.00073 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 234 time to evaluate : 0.695 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: A 122 GLN cc_start: 0.8305 (pt0) cc_final: 0.7911 (pp30) REVERT: A 139 GLU cc_start: 0.8159 (tt0) cc_final: 0.7161 (mp0) REVERT: A 157 MET cc_start: 0.8567 (mmm) cc_final: 0.7732 (mmm) REVERT: A 191 GLU cc_start: 0.7700 (mp0) cc_final: 0.7368 (mp0) REVERT: A 298 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.7760 (tp) REVERT: A 396 LEU cc_start: 0.9247 (tp) cc_final: 0.8983 (tt) REVERT: A 402 MET cc_start: 0.7770 (ttt) cc_final: 0.7379 (ttt) REVERT: A 409 PHE cc_start: 0.8004 (t80) cc_final: 0.7523 (t80) REVERT: B 122 GLN cc_start: 0.8305 (pt0) cc_final: 0.7906 (pp30) REVERT: B 139 GLU cc_start: 0.8156 (tt0) cc_final: 0.7161 (mp0) REVERT: B 157 MET cc_start: 0.8571 (mmm) cc_final: 0.7741 (mmm) REVERT: B 191 GLU cc_start: 0.7692 (mp0) cc_final: 0.7447 (mp0) REVERT: B 298 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.7765 (tp) REVERT: B 396 LEU cc_start: 0.9249 (tp) cc_final: 0.8999 (tt) REVERT: B 402 MET cc_start: 0.7769 (ttt) cc_final: 0.7373 (ttt) REVERT: B 409 PHE cc_start: 0.8013 (t80) cc_final: 0.7581 (t80) REVERT: C 2 LYS cc_start: 0.8696 (mmtm) cc_final: 0.7975 (mmtp) REVERT: C 18 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8760 (tp) REVERT: C 122 GLN cc_start: 0.8288 (pt0) cc_final: 0.7914 (pp30) REVERT: C 157 MET cc_start: 0.8566 (mmm) cc_final: 0.7688 (mmm) REVERT: C 191 GLU cc_start: 0.7956 (mp0) cc_final: 0.7713 (mp0) REVERT: C 298 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7750 (tp) REVERT: C 496 ASP cc_start: 0.7593 (p0) cc_final: 0.7104 (p0) REVERT: D 18 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8754 (tp) REVERT: D 122 GLN cc_start: 0.8293 (pt0) cc_final: 0.7919 (pp30) REVERT: D 139 GLU cc_start: 0.8149 (tt0) cc_final: 0.6988 (mp0) REVERT: D 157 MET cc_start: 0.8569 (mmm) cc_final: 0.7688 (mmm) REVERT: D 298 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.7749 (tp) REVERT: D 409 PHE cc_start: 0.7984 (t80) cc_final: 0.7728 (t80) REVERT: D 436 MET cc_start: 0.7892 (tpp) cc_final: 0.7615 (tpp) REVERT: D 496 ASP cc_start: 0.7738 (p0) cc_final: 0.7292 (p0) outliers start: 70 outliers final: 58 residues processed: 289 average time/residue: 0.1171 time to fit residues: 54.3797 Evaluate side-chains 279 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 215 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 150 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN B 87 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN B 526 HIS C 237 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN ** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 ASN D 443 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.121451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096958 restraints weight = 39880.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.100692 restraints weight = 20705.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103316 restraints weight = 13481.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105112 restraints weight = 9999.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.106373 restraints weight = 8077.925| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18264 Z= 0.164 Angle : 0.685 10.518 24760 Z= 0.341 Chirality : 0.047 0.197 2752 Planarity : 0.005 0.057 3176 Dihedral : 8.516 59.896 2580 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.12 % Allowed : 19.60 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.17), residues: 2228 helix: -0.40 (0.17), residues: 848 sheet: -2.59 (0.25), residues: 364 loop : -1.30 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 389 TYR 0.013 0.002 TYR B 468 PHE 0.026 0.002 PHE B 50 TRP 0.011 0.001 TRP A 124 HIS 0.005 0.001 HIS D 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (18260) covalent geometry : angle 0.68519 / 0.34 (24760) hydrogen bonds : bond 0.03087 / 2.13 ( 488) hydrogen bonds : angle 4.40671 / 3.09 ( 1416) Misc. bond : bond 0.00062 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 221 time to evaluate : 0.515 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: symmetry clash REVERT: A 122 GLN cc_start: 0.8306 (pt0) cc_final: 0.7928 (pp30) REVERT: A 139 GLU cc_start: 0.8176 (tt0) cc_final: 0.7228 (mp0) REVERT: A 157 MET cc_start: 0.8664 (mmm) cc_final: 0.7921 (mmm) REVERT: A 191 GLU cc_start: 0.7689 (mp0) cc_final: 0.7388 (mp0) REVERT: A 298 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.7674 (tp) REVERT: A 396 LEU cc_start: 0.9304 (tp) cc_final: 0.9050 (tt) REVERT: A 402 MET cc_start: 0.7843 (ttt) cc_final: 0.7399 (ttt) REVERT: A 409 PHE cc_start: 0.8027 (t80) cc_final: 0.7601 (t80) REVERT: B 122 GLN cc_start: 0.8311 (pt0) cc_final: 0.7931 (pp30) REVERT: B 139 GLU cc_start: 0.8164 (tt0) cc_final: 0.7227 (mp0) REVERT: B 157 MET cc_start: 0.8656 (mmm) cc_final: 0.7880 (mmm) REVERT: B 191 GLU cc_start: 0.7674 (mp0) cc_final: 0.7373 (mp0) REVERT: B 237 ASN cc_start: 0.8814 (m-40) cc_final: 0.8508 (t0) REVERT: B 298 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7677 (tp) REVERT: B 396 LEU cc_start: 0.9294 (tp) cc_final: 0.9044 (tt) REVERT: B 402 MET cc_start: 0.7825 (ttt) cc_final: 0.7386 (ttt) REVERT: B 409 PHE cc_start: 0.8150 (t80) cc_final: 0.7770 (t80) REVERT: C 18 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8770 (tp) REVERT: C 122 GLN cc_start: 0.8313 (pt0) cc_final: 0.7937 (pp30) REVERT: C 191 GLU cc_start: 0.7988 (mp0) cc_final: 0.7715 (mp0) REVERT: C 298 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7711 (tp) REVERT: C 496 ASP cc_start: 0.7522 (p0) cc_final: 0.7071 (p0) REVERT: D 18 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8801 (tp) REVERT: D 122 GLN cc_start: 0.8317 (pt0) cc_final: 0.7942 (pp30) REVERT: D 139 GLU cc_start: 0.8152 (tt0) cc_final: 0.7063 (mp0) REVERT: D 298 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7680 (tp) REVERT: D 409 PHE cc_start: 0.8113 (t80) cc_final: 0.7849 (t80) REVERT: D 496 ASP cc_start: 0.7804 (p0) cc_final: 0.7341 (p0) outliers start: 80 outliers final: 65 residues processed: 284 average time/residue: 0.1177 time to fit residues: 53.3627 Evaluate side-chains 278 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 207 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 215 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN D 87 ASN D 167 GLN D 192 GLN D 237 ASN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.122842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098292 restraints weight = 39502.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.102082 restraints weight = 20551.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.104674 restraints weight = 13354.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.106489 restraints weight = 9947.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.107778 restraints weight = 8046.065| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18264 Z= 0.129 Angle : 0.682 10.283 24760 Z= 0.335 Chirality : 0.046 0.190 2752 Planarity : 0.004 0.058 3176 Dihedral : 8.224 59.979 2580 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.14 % Allowed : 21.35 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.17), residues: 2228 helix: -0.26 (0.18), residues: 852 sheet: -2.58 (0.25), residues: 376 loop : -1.07 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 311 TYR 0.012 0.001 TYR C 42 PHE 0.019 0.001 PHE B 50 TRP 0.010 0.001 TRP A 124 HIS 0.005 0.001 HIS D 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (18260) covalent geometry : angle 0.68181 / 0.33 (24760) hydrogen bonds : bond 0.02881 / 1.97 ( 488) hydrogen bonds : angle 4.28298 / 3.01 ( 1416) Misc. bond : bond 0.00077 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 215 time to evaluate : 0.673 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: A 122 GLN cc_start: 0.8288 (pt0) cc_final: 0.7879 (pp30) REVERT: A 139 GLU cc_start: 0.8021 (tt0) cc_final: 0.7098 (mp0) REVERT: A 191 GLU cc_start: 0.7699 (mp0) cc_final: 0.7401 (mp0) REVERT: A 298 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7550 (tp) REVERT: A 396 LEU cc_start: 0.9265 (tp) cc_final: 0.8975 (tt) REVERT: A 409 PHE cc_start: 0.8029 (t80) cc_final: 0.7590 (t80) REVERT: A 436 MET cc_start: 0.7904 (tpp) cc_final: 0.7627 (tpp) REVERT: B 122 GLN cc_start: 0.8287 (pt0) cc_final: 0.7874 (pp30) REVERT: B 139 GLU cc_start: 0.8016 (tt0) cc_final: 0.7100 (mp0) REVERT: B 191 GLU cc_start: 0.7690 (mp0) cc_final: 0.7390 (mp0) REVERT: B 298 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7557 (tp) REVERT: B 396 LEU cc_start: 0.9255 (tp) cc_final: 0.8976 (tt) REVERT: B 409 PHE cc_start: 0.8071 (t80) cc_final: 0.7645 (t80) REVERT: C 18 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8806 (tp) REVERT: C 122 GLN cc_start: 0.8275 (pt0) cc_final: 0.7848 (pp30) REVERT: C 157 MET cc_start: 0.8466 (mmm) cc_final: 0.7634 (mmm) REVERT: C 191 GLU cc_start: 0.7973 (mp0) cc_final: 0.7684 (mp0) REVERT: C 298 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7564 (tp) REVERT: C 436 MET cc_start: 0.7892 (tpp) cc_final: 0.7622 (tpp) REVERT: C 496 ASP cc_start: 0.7534 (p0) cc_final: 0.7087 (p0) REVERT: D 2 LYS cc_start: 0.8989 (mmtm) cc_final: 0.7953 (mmtp) REVERT: D 18 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8803 (tp) REVERT: D 122 GLN cc_start: 0.8292 (pt0) cc_final: 0.7873 (pp30) REVERT: D 139 GLU cc_start: 0.8225 (tt0) cc_final: 0.7046 (mp0) REVERT: D 157 MET cc_start: 0.8437 (mmm) cc_final: 0.7583 (mmm) REVERT: D 298 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7545 (tp) REVERT: D 409 PHE cc_start: 0.8058 (t80) cc_final: 0.7809 (t80) REVERT: D 436 MET cc_start: 0.7936 (tpp) cc_final: 0.7665 (tpp) REVERT: D 496 ASP cc_start: 0.7733 (p0) cc_final: 0.7275 (p0) outliers start: 61 outliers final: 52 residues processed: 262 average time/residue: 0.1200 time to fit residues: 50.0939 Evaluate side-chains 261 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 68 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 151 optimal weight: 0.0050 chunk 8 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.121416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096725 restraints weight = 39975.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.100473 restraints weight = 20804.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.103059 restraints weight = 13536.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104849 restraints weight = 10093.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.106132 restraints weight = 8180.684| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18264 Z= 0.163 Angle : 0.733 11.131 24760 Z= 0.358 Chirality : 0.049 0.313 2752 Planarity : 0.005 0.058 3176 Dihedral : 8.057 59.458 2580 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.19 % Allowed : 22.17 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2228 helix: -0.21 (0.18), residues: 852 sheet: -2.57 (0.25), residues: 376 loop : -1.05 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 311 TYR 0.014 0.002 TYR B 468 PHE 0.020 0.001 PHE B 50 TRP 0.011 0.001 TRP A 124 HIS 0.004 0.001 HIS C 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (18260) covalent geometry : angle 0.73305 / 0.36 (24760) hydrogen bonds : bond 0.02971 / 2.02 ( 488) hydrogen bonds : angle 4.34310 / 3.04 ( 1416) Misc. bond : bond 0.00069 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 0.543 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: symmetry clash REVERT: A 122 GLN cc_start: 0.8308 (pt0) cc_final: 0.7893 (pp30) REVERT: A 139 GLU cc_start: 0.8035 (tt0) cc_final: 0.7119 (mp0) REVERT: A 157 MET cc_start: 0.8407 (mmp) cc_final: 0.7656 (mmm) REVERT: A 191 GLU cc_start: 0.7687 (mp0) cc_final: 0.7397 (mp0) REVERT: A 298 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7485 (tp) REVERT: A 396 LEU cc_start: 0.9251 (tp) cc_final: 0.8972 (tt) REVERT: A 409 PHE cc_start: 0.8070 (t80) cc_final: 0.7742 (t80) REVERT: A 496 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6370 (t70) REVERT: B 122 GLN cc_start: 0.8309 (pt0) cc_final: 0.7890 (pp30) REVERT: B 139 GLU cc_start: 0.8049 (tt0) cc_final: 0.7121 (mp0) REVERT: B 157 MET cc_start: 0.8601 (mmm) cc_final: 0.7786 (mmm) REVERT: B 191 GLU cc_start: 0.7686 (mp0) cc_final: 0.7391 (mp0) REVERT: B 237 ASN cc_start: 0.8809 (m-40) cc_final: 0.8495 (t0) REVERT: B 298 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7503 (tp) REVERT: B 396 LEU cc_start: 0.9233 (tp) cc_final: 0.8952 (tt) REVERT: B 409 PHE cc_start: 0.8058 (t80) cc_final: 0.7722 (t80) REVERT: B 496 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6387 (t70) REVERT: C 18 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8832 (tp) REVERT: C 122 GLN cc_start: 0.8288 (pt0) cc_final: 0.7769 (pp30) REVERT: C 126 MET cc_start: 0.8758 (mmm) cc_final: 0.8553 (mmm) REVERT: C 157 MET cc_start: 0.8522 (mmm) cc_final: 0.7971 (mmt) REVERT: C 191 GLU cc_start: 0.8006 (mp0) cc_final: 0.7717 (mp0) REVERT: C 298 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7524 (tp) REVERT: C 436 MET cc_start: 0.7911 (tpp) cc_final: 0.7612 (tpp) REVERT: C 496 ASP cc_start: 0.7603 (p0) cc_final: 0.7151 (p0) REVERT: D 18 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8825 (tp) REVERT: D 122 GLN cc_start: 0.8309 (pt0) cc_final: 0.7897 (pp30) REVERT: D 157 MET cc_start: 0.8553 (mmm) cc_final: 0.7819 (mmt) REVERT: D 298 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7505 (tp) REVERT: D 409 PHE cc_start: 0.8132 (t80) cc_final: 0.7824 (t80) REVERT: D 496 ASP cc_start: 0.7817 (p0) cc_final: 0.7355 (p0) outliers start: 62 outliers final: 53 residues processed: 259 average time/residue: 0.1193 time to fit residues: 49.1349 Evaluate side-chains 261 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 132 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 216 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.122798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.098228 restraints weight = 39464.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.102007 restraints weight = 20508.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104619 restraints weight = 13346.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106460 restraints weight = 9908.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.107769 restraints weight = 7985.319| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18264 Z= 0.134 Angle : 0.718 11.072 24760 Z= 0.350 Chirality : 0.048 0.297 2752 Planarity : 0.004 0.058 3176 Dihedral : 7.668 59.219 2580 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.14 % Allowed : 22.27 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.17), residues: 2228 helix: -0.11 (0.18), residues: 856 sheet: -2.55 (0.25), residues: 376 loop : -1.08 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 311 TYR 0.012 0.002 TYR C 42 PHE 0.019 0.001 PHE B 50 TRP 0.010 0.001 TRP A 124 HIS 0.004 0.001 HIS C 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (18260) covalent geometry : angle 0.71797 / 0.35 (24760) hydrogen bonds : bond 0.02861 / 1.91 ( 488) hydrogen bonds : angle 4.26854 / 2.99 ( 1416) Misc. bond : bond 0.00062 / 0.03 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 213 time to evaluate : 0.687 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: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8245 (pt0) cc_final: 0.7773 (pp30) REVERT: A 139 GLU cc_start: 0.8062 (tt0) cc_final: 0.7124 (mp0) REVERT: A 157 MET cc_start: 0.8447 (mmp) cc_final: 0.7745 (mmm) REVERT: A 191 GLU cc_start: 0.7716 (mp0) cc_final: 0.7411 (mp0) REVERT: A 298 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7385 (tp) REVERT: A 396 LEU cc_start: 0.9211 (tp) cc_final: 0.8906 (tt) REVERT: A 409 PHE cc_start: 0.8092 (t80) cc_final: 0.7779 (t80) REVERT: A 436 MET cc_start: 0.7798 (tpp) cc_final: 0.7530 (tpp) REVERT: A 496 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6337 (t70) REVERT: B 122 GLN cc_start: 0.8245 (pt0) cc_final: 0.7766 (pp30) REVERT: B 139 GLU cc_start: 0.8072 (tt0) cc_final: 0.7129 (mp0) REVERT: B 157 MET cc_start: 0.8647 (mmm) cc_final: 0.7795 (mmm) REVERT: B 191 GLU cc_start: 0.7708 (mp0) cc_final: 0.7397 (mp0) REVERT: B 298 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7400 (tp) REVERT: B 396 LEU cc_start: 0.9229 (tp) cc_final: 0.8929 (tt) REVERT: B 409 PHE cc_start: 0.8069 (t80) cc_final: 0.7755 (t80) REVERT: B 436 MET cc_start: 0.7803 (tpp) cc_final: 0.7526 (tpp) REVERT: B 496 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6348 (t70) REVERT: C 18 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8827 (tp) REVERT: C 122 GLN cc_start: 0.8227 (pt0) cc_final: 0.7704 (pp30) REVERT: C 126 MET cc_start: 0.8740 (mmm) cc_final: 0.8535 (mmm) REVERT: C 157 MET cc_start: 0.8504 (mmm) cc_final: 0.7848 (mmt) REVERT: C 191 GLU cc_start: 0.7990 (mp0) cc_final: 0.7698 (mp0) REVERT: C 436 MET cc_start: 0.7929 (tpp) cc_final: 0.7656 (tpp) REVERT: C 496 ASP cc_start: 0.7543 (p0) cc_final: 0.7100 (p0) REVERT: D 18 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8818 (tp) REVERT: D 122 GLN cc_start: 0.8250 (pt0) cc_final: 0.7769 (pp30) REVERT: D 409 PHE cc_start: 0.8074 (t80) cc_final: 0.7809 (t80) REVERT: D 436 MET cc_start: 0.7717 (tpp) cc_final: 0.7457 (tpp) REVERT: D 496 ASP cc_start: 0.7737 (p0) cc_final: 0.7290 (p0) outliers start: 61 outliers final: 51 residues processed: 259 average time/residue: 0.1258 time to fit residues: 51.8032 Evaluate side-chains 256 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 199 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 97 optimal weight: 8.9990 chunk 155 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 53 optimal weight: 0.1980 chunk 69 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.124400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.099681 restraints weight = 39628.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.103513 restraints weight = 20747.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106148 restraints weight = 13537.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.107980 restraints weight = 10089.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109186 restraints weight = 8163.778| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18264 Z= 0.125 Angle : 0.730 12.368 24760 Z= 0.351 Chirality : 0.048 0.293 2752 Planarity : 0.004 0.058 3176 Dihedral : 7.280 58.806 2580 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.67 % Allowed : 22.84 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.18), residues: 2228 helix: 0.07 (0.18), residues: 832 sheet: -2.54 (0.24), residues: 380 loop : -1.00 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 389 TYR 0.013 0.001 TYR C 42 PHE 0.017 0.001 PHE B 50 TRP 0.008 0.001 TRP D 387 HIS 0.006 0.001 HIS A 480 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (18260) covalent geometry : angle 0.72976 / 0.35 (24760) hydrogen bonds : bond 0.02781 / 1.85 ( 488) hydrogen bonds : angle 4.21619 / 2.96 ( 1416) Misc. bond : bond 0.00060 / 0.03 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2941.46 seconds wall clock time: 51 minutes 54.48 seconds (3114.48 seconds total)