Starting phenix.real_space_refine on Sun Jul 5 02:31:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ul7_26594/07_2026/7ul7_26594.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ul7_26594/07_2026/7ul7_26594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ul7_26594/07_2026/7ul7_26594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ul7_26594/07_2026/7ul7_26594.map" model { file = "/net/cci-nas-00/data/ceres_data/7ul7_26594/07_2026/7ul7_26594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ul7_26594/07_2026/7ul7_26594.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ul7_26594/07_2026/7ul7_26594.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ul7_26594/07_2026/7ul7_26594.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9444 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 10986 2.51 5 N 2922 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17439 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 2 Chain: "D" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1579 Classifications: {'peptide': 205} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "E" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1621 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "A" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 2 Chain: "L" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1579 Classifications: {'peptide': 205} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "H" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1621 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "B" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 2 Chain: "F" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1579 Classifications: {'peptide': 205} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "G" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1621 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "c" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1225 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "b" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1225 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "a" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1225 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.07, per 1000 atoms: 0.23 Number of scatterers: 17439 At special positions: 0 Unit cell: (187.92, 178.848, 103.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 3420 8.00 N 2922 7.00 C 10986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 206 " distance=2.03 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.03 Simple disulfide: pdb=" SG CYS c 300 " - pdb=" SG CYS c 309 " distance=2.03 Simple disulfide: pdb=" SG CYS c 363 " - pdb=" SG CYS c 384 " distance=2.03 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.03 Simple disulfide: pdb=" SG CYS b 300 " - pdb=" SG CYS b 309 " distance=2.03 Simple disulfide: pdb=" SG CYS b 363 " - pdb=" SG CYS b 384 " distance=2.02 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.03 Simple disulfide: pdb=" SG CYS a 300 " - pdb=" SG CYS a 309 " distance=2.03 Simple disulfide: pdb=" SG CYS a 363 " - pdb=" SG CYS a 384 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 301 " - " ASN A 88 " " NAG A 302 " - " ASN A 108 " " NAG A 303 " - " ASN A 166 " " NAG A 304 " - " ASN A 223 " " NAG A 305 " - " ASN A 118 " " NAG B 301 " - " ASN B 108 " " NAG B 302 " - " ASN B 166 " " NAG B 303 " - " ASN B 223 " " NAG C 301 " - " ASN C 88 " " NAG C 302 " - " ASN C 108 " " NAG C 303 " - " ASN C 166 " " NAG C 304 " - " ASN C 223 " " NAG C 305 " - " ASN C 118 " " NAG I 1 " - " ASN C 78 " " NAG J 1 " - " ASN A 78 " " NAG K 1 " - " ASN B 78 " " NAG M 1 " - " ASN B 88 " " NAG a 501 " - " ASN a 389 " " NAG a 502 " - " ASN a 372 " " NAG a 503 " - " ASN a 394 " " NAG b 501 " - " ASN b 372 " " NAG b 502 " - " ASN b 389 " " NAG b 503 " - " ASN b 394 " " NAG c 501 " - " ASN c 372 " " NAG c 502 " - " ASN c 389 " " NAG c 503 " - " ASN c 394 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 793.9 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4068 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 37 sheets defined 19.5% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 132 through 143 removed outlier: 4.041A pdb=" N ILE C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.505A pdb=" N LYS C 160 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.594A pdb=" N GLY C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 removed outlier: 3.709A pdb=" N SER D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 130' Processing helix chain 'D' and resid 185 through 189 Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 211 through 214 Processing helix chain 'A' and resid 119 through 126 removed outlier: 4.167A pdb=" N ASN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 removed outlier: 4.204A pdb=" N ILE A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.675A pdb=" N LEU A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 242' Processing helix chain 'L' and resid 124 through 128 Processing helix chain 'L' and resid 186 through 190 removed outlier: 3.871A pdb=" N LYS L 190 " --> pdb=" O ASP L 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 211 through 214 Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.633A pdb=" N HIS B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 removed outlier: 3.925A pdb=" N ILE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 143 " --> pdb=" O PHE B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.673A pdb=" N LEU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 124 through 129 removed outlier: 3.815A pdb=" N LEU F 127 " --> pdb=" O ASP F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 4.051A pdb=" N GLU F 189 " --> pdb=" O LYS F 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 185 through 189' Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 197 through 199 No H-bonds generated for 'chain 'G' and resid 197 through 199' Processing helix chain 'G' and resid 212 through 214 No H-bonds generated for 'chain 'G' and resid 212 through 214' Processing helix chain 'c' and resid 293 through 298 Processing helix chain 'c' and resid 299 through 303 removed outlier: 3.621A pdb=" N LYS c 303 " --> pdb=" O CYS c 300 " (cutoff:3.500A) Processing helix chain 'c' and resid 308 through 324 removed outlier: 3.824A pdb=" N ARG c 323 " --> pdb=" O LYS c 319 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG c 324 " --> pdb=" O GLN c 320 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 344 removed outlier: 5.489A pdb=" N ASN c 341 " --> pdb=" O ASN c 337 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ALA c 342 " --> pdb=" O LYS c 338 " (cutoff:3.500A) Processing helix chain 'c' and resid 345 through 358 removed outlier: 3.987A pdb=" N ILE c 349 " --> pdb=" O ASN c 345 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET c 358 " --> pdb=" O LEU c 354 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 397 No H-bonds generated for 'chain 'c' and resid 395 through 397' Processing helix chain 'c' and resid 398 through 414 removed outlier: 3.964A pdb=" N ALA c 406 " --> pdb=" O ILE c 402 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN c 408 " --> pdb=" O GLN c 404 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU c 414 " --> pdb=" O ILE c 410 " (cutoff:3.500A) Processing helix chain 'b' and resid 293 through 298 Processing helix chain 'b' and resid 299 through 303 removed outlier: 3.714A pdb=" N GLU b 302 " --> pdb=" O LYS b 299 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS b 303 " --> pdb=" O CYS b 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 299 through 303' Processing helix chain 'b' and resid 307 through 325 removed outlier: 3.525A pdb=" N MET b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG b 323 " --> pdb=" O LYS b 319 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU b 325 " --> pdb=" O ALA b 321 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 338 Processing helix chain 'b' and resid 339 through 344 removed outlier: 3.708A pdb=" N LEU b 343 " --> pdb=" O ALA b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 345 through 358 removed outlier: 4.153A pdb=" N ILE b 349 " --> pdb=" O ASN b 345 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 397 No H-bonds generated for 'chain 'b' and resid 395 through 397' Processing helix chain 'b' and resid 398 through 414 removed outlier: 3.892A pdb=" N ALA b 406 " --> pdb=" O ILE b 402 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN b 408 " --> pdb=" O GLN b 404 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE b 410 " --> pdb=" O ALA b 406 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU b 414 " --> pdb=" O ILE b 410 " (cutoff:3.500A) Processing helix chain 'a' and resid 280 through 284 removed outlier: 3.600A pdb=" N LEU a 284 " --> pdb=" O ARG a 281 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 298 Processing helix chain 'a' and resid 299 through 303 removed outlier: 3.589A pdb=" N GLU a 302 " --> pdb=" O LYS a 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS a 303 " --> pdb=" O CYS a 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 299 through 303' Processing helix chain 'a' and resid 307 through 325 removed outlier: 3.542A pdb=" N LEU a 325 " --> pdb=" O ALA a 321 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 344 removed outlier: 6.095A pdb=" N ASN a 341 " --> pdb=" O ASN a 337 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA a 342 " --> pdb=" O LYS a 338 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 358 removed outlier: 4.003A pdb=" N ILE a 349 " --> pdb=" O ASN a 345 " (cutoff:3.500A) Processing helix chain 'a' and resid 394 through 397 Processing helix chain 'a' and resid 398 through 413 removed outlier: 4.001A pdb=" N ALA a 406 " --> pdb=" O ILE a 402 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN a 408 " --> pdb=" O GLN a 404 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET a 409 " --> pdb=" O GLN a 405 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE a 410 " --> pdb=" O ALA a 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 66 through 71 removed outlier: 3.740A pdb=" N LYS c 383 " --> pdb=" O TRP c 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 88 removed outlier: 3.550A pdb=" N CYS C 85 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS C 87 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N HIS C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 101 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 5 through 7 removed outlier: 4.064A pdb=" N CYS D 23 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE D 72 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.490A pdb=" N LEU D 11 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 104 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.490A pdb=" N LEU D 11 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 104 " --> pdb=" O TYR D 87 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 116 through 120 removed outlier: 6.120A pdb=" N TYR D 175 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 147 through 151 Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.470A pdb=" N GLN E 3 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.861A pdb=" N GLY E 10 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR E 60 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 130 through 134 removed outlier: 3.806A pdb=" N ASP E 154 " --> pdb=" O TYR E 186 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR E 186 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 161 through 164 Processing sheet with id=AB3, first strand: chain 'A' and resid 67 through 71 Processing sheet with id=AB4, first strand: chain 'A' and resid 83 through 88 removed outlier: 5.619A pdb=" N SER A 84 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG A 95 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR A 86 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR A 93 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN A 88 " --> pdb=" O HIS A 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.936A pdb=" N CYS L 23 " --> pdb=" O PHE L 72 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE L 72 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.558A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.686A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 116 through 120 removed outlier: 6.233A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 147 through 151 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.254A pdb=" N GLN H 3 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.592A pdb=" N GLY H 10 " --> pdb=" O ILE H 120 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.958A pdb=" N ASP H 154 " --> pdb=" O TYR H 186 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AC5, first strand: chain 'B' and resid 66 through 71 removed outlier: 4.410A pdb=" N ASN b 364 " --> pdb=" O TRP b 385 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TRP b 385 " --> pdb=" O ASN b 364 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N SER b 366 " --> pdb=" O LYS b 383 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N LYS b 383 " --> pdb=" O SER b 366 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.722A pdb=" N VAL B 163 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.450A pdb=" N LEU F 11 " --> pdb=" O GLU F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 46 through 50 removed outlier: 5.508A pdb=" N LEU F 47 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR F 91 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 116 through 120 removed outlier: 6.058A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 146 through 152 removed outlier: 3.979A pdb=" N VAL F 207 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS F 200 " --> pdb=" O SER F 205 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER F 205 " --> pdb=" O HIS F 200 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 6 through 8 removed outlier: 3.841A pdb=" N SER G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.921A pdb=" N GLY G 10 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N MET G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR G 60 " --> pdb=" O SER G 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 130 through 134 removed outlier: 4.858A pdb=" N ALA G 147 " --> pdb=" O VAL G 194 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL G 194 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLY G 149 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL G 192 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU G 151 " --> pdb=" O SER G 190 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER G 190 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS G 153 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU G 188 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 160 through 164 Processing sheet with id=AD7, first strand: chain 'c' and resid 278 through 279 Processing sheet with id=AD8, first strand: chain 'c' and resid 387 through 388 Processing sheet with id=AD9, first strand: chain 'b' and resid 278 through 279 Processing sheet with id=AE1, first strand: chain 'a' and resid 278 through 279 594 hydrogen bonds defined for protein. 1521 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: 3.10 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5517 1.35 - 1.47: 4696 1.47 - 1.59: 7445 1.59 - 1.72: 0 1.72 - 1.84: 162 Bond restraints: 17820 Sorted by residual: bond pdb=" C1 NAG a 503 " pdb=" O5 NAG a 503 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" CB PRO D 206 " pdb=" CG PRO D 206 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.57e+00 bond pdb=" CB PRO E 133 " pdb=" CG PRO E 133 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.86e+00 bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" C1 NAG B 303 " pdb=" O5 NAG B 303 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 17815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 23787 2.37 - 4.73: 340 4.73 - 7.10: 29 7.10 - 9.46: 3 9.46 - 11.83: 3 Bond angle restraints: 24162 Sorted by residual: angle pdb=" CA PRO D 206 " pdb=" N PRO D 206 " pdb=" CD PRO D 206 " ideal model delta sigma weight residual 112.00 105.30 6.70 1.40e+00 5.10e-01 2.29e+01 angle pdb=" CB MET C 133 " pdb=" CG MET C 133 " pdb=" SD MET C 133 " ideal model delta sigma weight residual 112.70 124.53 -11.83 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CA CYS A 154 " pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " ideal model delta sigma weight residual 114.40 122.52 -8.12 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CA GLU C 227 " pdb=" CB GLU C 227 " pdb=" CG GLU C 227 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CB LYS B 87 " pdb=" CG LYS B 87 " pdb=" CD LYS B 87 " ideal model delta sigma weight residual 111.30 117.93 -6.63 2.30e+00 1.89e-01 8.30e+00 ... (remaining 24157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 9206 16.14 - 32.27: 918 32.27 - 48.41: 228 48.41 - 64.55: 40 64.55 - 80.69: 18 Dihedral angle restraints: 10410 sinusoidal: 4086 harmonic: 6324 Sorted by residual: dihedral pdb=" CB CYS b 363 " pdb=" SG CYS b 363 " pdb=" SG CYS b 384 " pdb=" CB CYS b 384 " ideal model delta sinusoidal sigma weight residual -86.00 -147.60 61.60 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS a 363 " pdb=" SG CYS a 363 " pdb=" SG CYS a 384 " pdb=" CB CYS a 384 " ideal model delta sinusoidal sigma weight residual -86.00 -145.77 59.77 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CB CYS b 278 " pdb=" SG CYS b 278 " pdb=" SG CYS b 291 " pdb=" CB CYS b 291 " ideal model delta sinusoidal sigma weight residual -86.00 -27.29 -58.71 1 1.00e+01 1.00e-02 4.61e+01 ... (remaining 10407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2628 0.097 - 0.193: 143 0.193 - 0.290: 6 0.290 - 0.386: 3 0.386 - 0.483: 1 Chirality restraints: 2781 Sorted by residual: chirality pdb=" C1 NAG a 503 " pdb=" ND2 ASN a 394 " pdb=" C2 NAG a 503 " pdb=" O5 NAG a 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C 78 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 78 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 2778 not shown) Planarity restraints: 3047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 385 " 0.029 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP a 385 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP a 385 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP a 385 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP a 385 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 385 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP a 385 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 385 " 0.026 2.00e-02 2.50e+03 2.38e-02 1.41e+01 pdb=" CG TRP b 385 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP b 385 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP b 385 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP b 385 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP b 385 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP b 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 385 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 385 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP b 385 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 59 " -0.054 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO F 60 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.045 5.00e-02 4.00e+02 ... (remaining 3044 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 711 2.71 - 3.26: 17124 3.26 - 3.81: 26466 3.81 - 4.35: 31822 4.35 - 4.90: 54359 Nonbonded interactions: 130482 Sorted by model distance: nonbonded pdb=" OD1 ASP G 111 " pdb=" N VAL G 112 " model vdw 2.165 3.120 nonbonded pdb=" OD1 ASP E 111 " pdb=" N VAL E 112 " model vdw 2.180 3.120 nonbonded pdb=" O ASN C 184 " pdb=" NE2 GLN C 188 " model vdw 2.198 3.120 nonbonded pdb=" OG SER c 332 " pdb=" OE1 GLN c 334 " model vdw 2.205 3.040 nonbonded pdb=" O LEU L 127 " pdb=" NZ LYS L 185 " model vdw 2.210 3.120 ... (remaining 130477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 65 through 303) selection = chain 'B' selection = (chain 'C' and resid 65 through 303) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.100 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 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 : 0.005 0.094 17877 Z= 0.200 Angle : 0.735 20.954 24306 Z= 0.358 Chirality : 0.049 0.483 2781 Planarity : 0.005 0.083 3021 Dihedral : 13.722 80.686 6261 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.18), residues: 2124 helix: -1.18 (0.29), residues: 288 sheet: 0.36 (0.21), residues: 663 loop : -1.13 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 88 TYR 0.017 0.002 TYR G 155 PHE 0.036 0.002 PHE b 308 TRP 0.065 0.002 TRP a 385 HIS 0.011 0.001 HIS G 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (17820) covalent geometry : angle 0.68492 / 0.35 (24162) SS BOND : bond 0.00450 / 0.25 ( 27) SS BOND : angle 2.05153 / 1.20 ( 54) hydrogen bonds : bond 0.15785 / 10.60 ( 593) hydrogen bonds : angle 7.31152 / 5.05 ( 1521) link_BETA1-4 : bond 0.00092 / 0.05 ( 4) link_BETA1-4 : angle 2.47075 / 1.41 ( 12) link_NAG-ASN : bond 0.01121 / 0.77 ( 26) link_NAG-ASN : angle 4.39721 / 2.68 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7656 (t0) cc_final: 0.7438 (t0) REVERT: C 102 LEU cc_start: 0.7200 (mm) cc_final: 0.6989 (mp) REVERT: D 83 ASP cc_start: 0.7091 (m-30) cc_final: 0.6829 (m-30) REVERT: E 179 VAL cc_start: 0.8336 (p) cc_final: 0.8022 (m) REVERT: A 66 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6467 (tm-30) REVERT: A 103 GLU cc_start: 0.6635 (tt0) cc_final: 0.6375 (tt0) REVERT: A 221 ILE cc_start: 0.7135 (mp) cc_final: 0.6896 (mp) REVERT: L 174 THR cc_start: 0.7925 (m) cc_final: 0.7680 (m) REVERT: H 126 THR cc_start: 0.8315 (t) cc_final: 0.8103 (m) REVERT: H 211 LYS cc_start: 0.8289 (tppt) cc_final: 0.7898 (tppt) REVERT: B 87 LYS cc_start: 0.7058 (tppt) cc_final: 0.6551 (tppt) REVERT: c 383 LYS cc_start: 0.7574 (ptpp) cc_final: 0.7350 (ptpp) REVERT: b 383 LYS cc_start: 0.7203 (ptpp) cc_final: 0.6968 (ptpp) REVERT: a 283 MET cc_start: 0.6656 (tpt) cc_final: 0.6268 (mmm) REVERT: a 356 ASP cc_start: 0.7187 (t70) cc_final: 0.6953 (t0) REVERT: a 392 TYR cc_start: 0.6966 (m-80) cc_final: 0.6593 (m-80) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.1398 time to fit residues: 96.4054 Evaluate side-chains 445 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0070 chunk 212 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 GLN D 90 GLN E 6 GLN ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN A 126 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN G 35 ASN c 373 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.171959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.143315 restraints weight = 29024.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148067 restraints weight = 16337.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.151235 restraints weight = 10978.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.153204 restraints weight = 8268.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.154768 restraints weight = 6813.988| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17877 Z= 0.165 Angle : 0.718 19.515 24306 Z= 0.349 Chirality : 0.045 0.270 2781 Planarity : 0.005 0.072 3021 Dihedral : 4.815 22.760 2343 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.73 % Allowed : 10.47 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.18), residues: 2124 helix: -1.08 (0.29), residues: 312 sheet: 0.52 (0.21), residues: 642 loop : -1.00 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 99 TYR 0.026 0.001 TYR D 50 PHE 0.026 0.002 PHE a 261 TRP 0.026 0.002 TRP a 385 HIS 0.010 0.001 HIS G 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (17820) covalent geometry : angle 0.67166 / 0.34 (24162) SS BOND : bond 0.00518 / 0.30 ( 27) SS BOND : angle 1.76909 / 1.21 ( 54) hydrogen bonds : bond 0.05072 / 3.43 ( 593) hydrogen bonds : angle 6.44281 / 4.47 ( 1521) link_BETA1-4 : bond 0.00259 / 0.13 ( 4) link_BETA1-4 : angle 1.69620 / 0.97 ( 12) link_NAG-ASN : bond 0.00774 / 0.50 ( 26) link_NAG-ASN : angle 4.28286 / 2.59 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 451 time to evaluate : 0.636 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: C 133 MET cc_start: 0.7371 (mmm) cc_final: 0.6677 (tpt) REVERT: C 195 TRP cc_start: 0.7122 (t60) cc_final: 0.6880 (t60) REVERT: D 83 ASP cc_start: 0.7331 (m-30) cc_final: 0.6861 (m-30) REVERT: D 107 GLU cc_start: 0.6329 (pt0) cc_final: 0.5949 (pt0) REVERT: E 83 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7559 (tp-100) REVERT: E 179 VAL cc_start: 0.8352 (p) cc_final: 0.8047 (m) REVERT: A 66 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6482 (tm-30) REVERT: A 103 GLU cc_start: 0.6506 (tt0) cc_final: 0.6261 (tt0) REVERT: L 82 GLU cc_start: 0.6974 (mp0) cc_final: 0.6610 (mp0) REVERT: H 88 ARG cc_start: 0.7115 (mmm160) cc_final: 0.6730 (mmm160) REVERT: H 211 LYS cc_start: 0.8242 (tppt) cc_final: 0.7857 (tppt) REVERT: B 81 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6673 (mtm) REVERT: B 87 LYS cc_start: 0.6976 (tppt) cc_final: 0.6717 (tppt) REVERT: B 88 ASN cc_start: 0.7706 (p0) cc_final: 0.7490 (p0) REVERT: B 165 TYR cc_start: 0.7829 (m-80) cc_final: 0.7614 (m-10) REVERT: B 236 SER cc_start: 0.7365 (t) cc_final: 0.7125 (m) REVERT: F 6 GLN cc_start: 0.6770 (mp10) cc_final: 0.6515 (mp10) REVERT: F 38 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7694 (tp40) REVERT: G 110 MET cc_start: 0.6284 (mpp) cc_final: 0.6076 (mpp) REVERT: G 118 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7613 (p) REVERT: b 320 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.6728 (mp10) REVERT: a 283 MET cc_start: 0.6206 (tpt) cc_final: 0.5983 (mmm) REVERT: a 356 ASP cc_start: 0.7179 (t70) cc_final: 0.6887 (t0) REVERT: a 367 LYS cc_start: 0.7873 (ptmt) cc_final: 0.7643 (ptmt) REVERT: a 392 TYR cc_start: 0.6960 (m-80) cc_final: 0.6623 (m-80) outliers start: 33 outliers final: 20 residues processed: 461 average time/residue: 0.1274 time to fit residues: 88.7343 Evaluate side-chains 460 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 436 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain a residue 295 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 123 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 130 optimal weight: 0.4980 chunk 185 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 102 HIS ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS c 408 ASN a 352 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.170685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140935 restraints weight = 29263.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.145958 restraints weight = 15956.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149289 restraints weight = 10552.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.151398 restraints weight = 7882.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.152992 restraints weight = 6448.927| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17877 Z= 0.209 Angle : 0.716 19.001 24306 Z= 0.348 Chirality : 0.045 0.303 2781 Planarity : 0.005 0.068 3021 Dihedral : 4.865 24.380 2343 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.72 % Allowed : 13.45 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.18), residues: 2124 helix: -1.18 (0.28), residues: 312 sheet: 0.39 (0.21), residues: 672 loop : -1.04 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 99 TYR 0.025 0.002 TYR D 50 PHE 0.020 0.002 PHE a 261 TRP 0.029 0.002 TRP a 385 HIS 0.009 0.001 HIS G 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (17820) covalent geometry : angle 0.67072 / 0.34 (24162) SS BOND : bond 0.00537 / 0.31 ( 27) SS BOND : angle 1.58992 / 0.92 ( 54) hydrogen bonds : bond 0.04893 / 3.29 ( 593) hydrogen bonds : angle 6.31133 / 4.38 ( 1521) link_BETA1-4 : bond 0.00197 / 0.10 ( 4) link_BETA1-4 : angle 1.78692 / 1.01 ( 12) link_NAG-ASN : bond 0.00747 / 0.47 ( 26) link_NAG-ASN : angle 4.24538 / 2.53 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 441 time to evaluate : 0.639 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: C 87 LYS cc_start: 0.6919 (mmmt) cc_final: 0.6201 (tppt) REVERT: C 133 MET cc_start: 0.7683 (mmm) cc_final: 0.7319 (mmm) REVERT: C 154 CYS cc_start: 0.3005 (OUTLIER) cc_final: 0.2626 (p) REVERT: D 83 ASP cc_start: 0.7390 (m-30) cc_final: 0.6901 (m-30) REVERT: D 107 GLU cc_start: 0.6481 (pt0) cc_final: 0.6005 (pt0) REVERT: E 30 LYS cc_start: 0.7705 (ptmt) cc_final: 0.7253 (ptmm) REVERT: E 83 GLN cc_start: 0.7844 (tp-100) cc_final: 0.7606 (tp-100) REVERT: E 179 VAL cc_start: 0.8360 (p) cc_final: 0.8050 (m) REVERT: A 66 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6512 (tm-30) REVERT: A 103 GLU cc_start: 0.6676 (tt0) cc_final: 0.6396 (tt0) REVERT: H 54 ARG cc_start: 0.7720 (ptt180) cc_final: 0.7457 (ptp-170) REVERT: H 88 ARG cc_start: 0.7203 (mmm160) cc_final: 0.6873 (mmm160) REVERT: H 211 LYS cc_start: 0.8312 (tppt) cc_final: 0.7889 (tppt) REVERT: B 236 SER cc_start: 0.7518 (t) cc_final: 0.7272 (m) REVERT: G 118 THR cc_start: 0.8008 (p) cc_final: 0.7739 (p) REVERT: b 320 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.6867 (mp10) REVERT: b 378 ARG cc_start: 0.5887 (ttt180) cc_final: 0.5661 (ttt180) REVERT: a 356 ASP cc_start: 0.7247 (t70) cc_final: 0.6881 (t0) REVERT: a 392 TYR cc_start: 0.7061 (m-80) cc_final: 0.6790 (m-80) outliers start: 52 outliers final: 32 residues processed: 457 average time/residue: 0.1353 time to fit residues: 92.7479 Evaluate side-chains 469 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 435 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 279 LEU Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 30 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 170 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 190 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 91 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.168905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139290 restraints weight = 29209.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.144295 restraints weight = 15861.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.147636 restraints weight = 10454.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149758 restraints weight = 7805.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.151437 restraints weight = 6386.763| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17877 Z= 0.228 Angle : 0.729 18.828 24306 Z= 0.354 Chirality : 0.046 0.314 2781 Planarity : 0.005 0.065 3021 Dihedral : 4.956 25.880 2343 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.35 % Allowed : 15.59 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 2124 helix: -1.31 (0.28), residues: 312 sheet: 0.29 (0.21), residues: 678 loop : -1.08 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 99 TYR 0.025 0.002 TYR D 50 PHE 0.030 0.002 PHE a 261 TRP 0.028 0.002 TRP a 385 HIS 0.008 0.001 HIS G 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.23 (17820) covalent geometry : angle 0.68599 / 0.34 (24162) SS BOND : bond 0.00549 / 0.31 ( 27) SS BOND : angle 1.52677 / 0.87 ( 54) hydrogen bonds : bond 0.04774 / 3.20 ( 593) hydrogen bonds : angle 6.30120 / 4.37 ( 1521) link_BETA1-4 : bond 0.00241 / 0.12 ( 4) link_BETA1-4 : angle 1.83672 / 1.02 ( 12) link_NAG-ASN : bond 0.00745 / 0.47 ( 26) link_NAG-ASN : angle 4.19823 / 2.51 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 438 time to evaluate : 0.643 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: C 77 LEU cc_start: 0.8465 (mt) cc_final: 0.8192 (mp) REVERT: C 133 MET cc_start: 0.7787 (mmm) cc_final: 0.7518 (mmm) REVERT: C 154 CYS cc_start: 0.3018 (OUTLIER) cc_final: 0.2592 (p) REVERT: D 83 ASP cc_start: 0.7415 (m-30) cc_final: 0.6949 (m-30) REVERT: D 107 GLU cc_start: 0.6636 (pt0) cc_final: 0.6120 (pt0) REVERT: E 30 LYS cc_start: 0.7860 (ptmt) cc_final: 0.7363 (ptmm) REVERT: E 80 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.6036 (pt) REVERT: E 83 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7648 (tp-100) REVERT: E 179 VAL cc_start: 0.8354 (p) cc_final: 0.8033 (m) REVERT: A 66 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6549 (tm-30) REVERT: A 103 GLU cc_start: 0.6681 (tt0) cc_final: 0.6413 (tt0) REVERT: H 80 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6607 (tt) REVERT: H 88 ARG cc_start: 0.7202 (mmm160) cc_final: 0.6922 (mmm160) REVERT: H 211 LYS cc_start: 0.8333 (tppt) cc_final: 0.7895 (tppt) REVERT: B 133 MET cc_start: 0.7569 (tpp) cc_final: 0.6774 (tpt) REVERT: B 236 SER cc_start: 0.7554 (t) cc_final: 0.7288 (m) REVERT: G 2 VAL cc_start: 0.8119 (p) cc_final: 0.7826 (p) REVERT: G 118 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7759 (p) REVERT: c 299 LYS cc_start: 0.7577 (mtmm) cc_final: 0.7279 (mtmm) REVERT: b 307 GLU cc_start: 0.7790 (tp30) cc_final: 0.7353 (tp30) REVERT: b 320 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6873 (mp10) REVERT: b 334 GLN cc_start: 0.7242 (mp10) cc_final: 0.7040 (mp10) REVERT: a 356 ASP cc_start: 0.7238 (t70) cc_final: 0.6838 (t0) REVERT: a 392 TYR cc_start: 0.7136 (m-80) cc_final: 0.6896 (m-80) REVERT: a 409 MET cc_start: 0.6443 (mtt) cc_final: 0.6242 (mtt) outliers start: 64 outliers final: 47 residues processed: 457 average time/residue: 0.1387 time to fit residues: 95.5094 Evaluate side-chains 484 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 432 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 6 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 208 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 148 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 131 optimal weight: 0.0970 chunk 90 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 91 HIS E 6 GLN E 102 HIS A 126 ASN A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 229 HIS G 3 GLN c 373 HIS c 408 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.170517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.141748 restraints weight = 28944.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.146477 restraints weight = 16345.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.149628 restraints weight = 11027.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151571 restraints weight = 8334.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.153198 restraints weight = 6911.377| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17877 Z= 0.171 Angle : 0.691 18.629 24306 Z= 0.335 Chirality : 0.045 0.299 2781 Planarity : 0.005 0.062 3021 Dihedral : 4.832 24.868 2343 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.51 % Allowed : 17.11 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.18), residues: 2124 helix: -1.17 (0.29), residues: 312 sheet: 0.27 (0.21), residues: 684 loop : -1.04 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 378 TYR 0.024 0.002 TYR D 50 PHE 0.025 0.001 PHE a 261 TRP 0.025 0.002 TRP C 226 HIS 0.007 0.001 HIS G 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (17820) covalent geometry : angle 0.64743 / 0.32 (24162) SS BOND : bond 0.00479 / 0.27 ( 27) SS BOND : angle 1.40041 / 0.80 ( 54) hydrogen bonds : bond 0.04266 / 2.87 ( 593) hydrogen bonds : angle 6.13556 / 4.26 ( 1521) link_BETA1-4 : bond 0.00347 / 0.17 ( 4) link_BETA1-4 : angle 1.75225 / 0.98 ( 12) link_NAG-ASN : bond 0.00784 / 0.49 ( 26) link_NAG-ASN : angle 4.15609 / 2.51 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 437 time to evaluate : 0.665 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: C 103 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6691 (mm-30) REVERT: C 154 CYS cc_start: 0.2908 (OUTLIER) cc_final: 0.2513 (p) REVERT: D 83 ASP cc_start: 0.7436 (m-30) cc_final: 0.6985 (m-30) REVERT: D 107 GLU cc_start: 0.6569 (pt0) cc_final: 0.6109 (pt0) REVERT: E 80 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5998 (pt) REVERT: E 83 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7632 (tp-100) REVERT: E 179 VAL cc_start: 0.8311 (p) cc_final: 0.7994 (m) REVERT: A 66 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6599 (tm-30) REVERT: A 68 GLN cc_start: 0.7585 (mt0) cc_final: 0.7077 (mt0) REVERT: A 103 GLU cc_start: 0.6565 (tt0) cc_final: 0.6311 (tt0) REVERT: H 80 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6515 (tt) REVERT: H 88 ARG cc_start: 0.7142 (mmm160) cc_final: 0.6890 (mmm160) REVERT: H 99 ARG cc_start: 0.8241 (ttp-170) cc_final: 0.8014 (ttp-170) REVERT: H 211 LYS cc_start: 0.8295 (tppt) cc_final: 0.7871 (tppt) REVERT: B 133 MET cc_start: 0.7532 (tpp) cc_final: 0.6761 (tpt) REVERT: B 236 SER cc_start: 0.7498 (t) cc_final: 0.7245 (m) REVERT: F 207 VAL cc_start: 0.5574 (t) cc_final: 0.5152 (p) REVERT: G 2 VAL cc_start: 0.8144 (p) cc_final: 0.7841 (p) REVERT: G 118 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7680 (p) REVERT: c 299 LYS cc_start: 0.7560 (mtmm) cc_final: 0.7260 (mtmm) REVERT: c 313 ARG cc_start: 0.6588 (ttm-80) cc_final: 0.6388 (ttm-80) REVERT: b 307 GLU cc_start: 0.7797 (tp30) cc_final: 0.7367 (tp30) REVERT: b 320 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6989 (mp10) REVERT: a 307 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7214 (mm-30) REVERT: a 356 ASP cc_start: 0.7195 (t70) cc_final: 0.6862 (t0) REVERT: a 392 TYR cc_start: 0.7102 (m-80) cc_final: 0.6859 (m-80) outliers start: 67 outliers final: 47 residues processed: 460 average time/residue: 0.1332 time to fit residues: 93.1474 Evaluate side-chains 479 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 427 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 178 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 192 optimal weight: 0.3980 chunk 204 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 180 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 91 HIS E 102 HIS A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS c 373 HIS c 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.169108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139370 restraints weight = 29004.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.144403 restraints weight = 15828.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.147705 restraints weight = 10469.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.149872 restraints weight = 7846.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151396 restraints weight = 6423.506| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17877 Z= 0.223 Angle : 0.730 18.460 24306 Z= 0.354 Chirality : 0.046 0.306 2781 Planarity : 0.005 0.060 3021 Dihedral : 4.959 25.757 2343 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.82 % Allowed : 17.95 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 2124 helix: -1.25 (0.28), residues: 312 sheet: 0.25 (0.21), residues: 684 loop : -1.07 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 13 TYR 0.028 0.002 TYR a 365 PHE 0.022 0.002 PHE a 261 TRP 0.017 0.002 TRP D 98 HIS 0.006 0.001 HIS G 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (17820) covalent geometry : angle 0.68821 / 0.34 (24162) SS BOND : bond 0.00542 / 0.31 ( 27) SS BOND : angle 1.51210 / 0.88 ( 54) hydrogen bonds : bond 0.04581 / 3.07 ( 593) hydrogen bonds : angle 6.19510 / 4.30 ( 1521) link_BETA1-4 : bond 0.00266 / 0.13 ( 4) link_BETA1-4 : angle 1.86583 / 1.04 ( 12) link_NAG-ASN : bond 0.00751 / 0.48 ( 26) link_NAG-ASN : angle 4.12808 / 2.47 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 432 time to evaluate : 0.800 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: C 133 MET cc_start: 0.7690 (mmm) cc_final: 0.6563 (tpt) REVERT: C 154 CYS cc_start: 0.3101 (OUTLIER) cc_final: 0.2658 (p) REVERT: D 83 ASP cc_start: 0.7439 (m-30) cc_final: 0.6986 (m-30) REVERT: D 107 GLU cc_start: 0.6599 (pt0) cc_final: 0.6129 (pt0) REVERT: E 80 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5970 (pt) REVERT: E 83 GLN cc_start: 0.7959 (tp-100) cc_final: 0.7659 (tp-100) REVERT: E 179 VAL cc_start: 0.8319 (p) cc_final: 0.7995 (m) REVERT: A 66 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6554 (tm-30) REVERT: A 68 GLN cc_start: 0.7575 (mt0) cc_final: 0.7026 (mt0) REVERT: H 54 ARG cc_start: 0.7703 (ptp-170) cc_final: 0.7351 (ptt180) REVERT: H 88 ARG cc_start: 0.7238 (mmm160) cc_final: 0.6909 (mmm160) REVERT: H 211 LYS cc_start: 0.8343 (tppt) cc_final: 0.7903 (tppt) REVERT: B 133 MET cc_start: 0.7674 (tpp) cc_final: 0.6903 (tpt) REVERT: B 236 SER cc_start: 0.7570 (t) cc_final: 0.7255 (m) REVERT: G 118 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7731 (p) REVERT: c 299 LYS cc_start: 0.7581 (mtmm) cc_final: 0.7285 (mtmm) REVERT: c 313 ARG cc_start: 0.6668 (ttm-80) cc_final: 0.6400 (ttm-80) REVERT: b 320 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6928 (mp10) REVERT: a 356 ASP cc_start: 0.7214 (t70) cc_final: 0.6835 (t0) REVERT: a 392 TYR cc_start: 0.7140 (m-80) cc_final: 0.6892 (m-80) outliers start: 73 outliers final: 63 residues processed: 459 average time/residue: 0.1252 time to fit residues: 87.4408 Evaluate side-chains 493 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 426 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 409 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 161 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 212 optimal weight: 0.9990 chunk 182 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 93 optimal weight: 0.0470 chunk 60 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS c 373 HIS c 408 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.169296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140384 restraints weight = 28993.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.145116 restraints weight = 16345.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.148223 restraints weight = 11040.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.150431 restraints weight = 8385.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.151825 restraints weight = 6848.102| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17877 Z= 0.195 Angle : 0.722 18.404 24306 Z= 0.348 Chirality : 0.046 0.302 2781 Planarity : 0.005 0.057 3021 Dihedral : 4.936 25.472 2343 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.19 % Allowed : 18.68 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.18), residues: 2124 helix: -1.21 (0.29), residues: 312 sheet: 0.24 (0.21), residues: 684 loop : -1.05 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 13 TYR 0.024 0.002 TYR D 50 PHE 0.019 0.002 PHE a 261 TRP 0.014 0.002 TRP L 36 HIS 0.006 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (17820) covalent geometry : angle 0.67536 / 0.34 (24162) SS BOND : bond 0.00513 / 0.29 ( 27) SS BOND : angle 1.44074 / 0.84 ( 54) hydrogen bonds : bond 0.04345 / 2.91 ( 593) hydrogen bonds : angle 6.17365 / 4.28 ( 1521) link_BETA1-4 : bond 0.00323 / 0.16 ( 4) link_BETA1-4 : angle 1.86458 / 1.05 ( 12) link_NAG-ASN : bond 0.00767 / 0.49 ( 26) link_NAG-ASN : angle 4.36648 / 2.62 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 423 time to evaluate : 0.586 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: C 133 MET cc_start: 0.7671 (mmm) cc_final: 0.6581 (tpt) REVERT: C 154 CYS cc_start: 0.2957 (OUTLIER) cc_final: 0.2528 (p) REVERT: D 83 ASP cc_start: 0.7469 (m-30) cc_final: 0.7043 (m-30) REVERT: D 107 GLU cc_start: 0.6527 (pt0) cc_final: 0.6082 (pt0) REVERT: E 80 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.6026 (pt) REVERT: E 83 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7621 (tp-100) REVERT: E 179 VAL cc_start: 0.8283 (p) cc_final: 0.7963 (m) REVERT: A 66 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6562 (tm-30) REVERT: A 68 GLN cc_start: 0.7541 (mt0) cc_final: 0.7010 (mt0) REVERT: A 87 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.6148 (ptpp) REVERT: H 88 ARG cc_start: 0.7191 (mmm160) cc_final: 0.6854 (mmm160) REVERT: H 211 LYS cc_start: 0.8314 (tppt) cc_final: 0.7875 (tppt) REVERT: B 133 MET cc_start: 0.7697 (tpp) cc_final: 0.7070 (tpt) REVERT: B 236 SER cc_start: 0.7572 (t) cc_final: 0.7244 (m) REVERT: F 164 SER cc_start: 0.7838 (m) cc_final: 0.7009 (t) REVERT: G 118 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7678 (p) REVERT: c 299 LYS cc_start: 0.7575 (mtmm) cc_final: 0.7284 (mtmm) REVERT: c 313 ARG cc_start: 0.6700 (ttm-80) cc_final: 0.6423 (ttm-80) REVERT: b 320 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6951 (mp10) REVERT: a 356 ASP cc_start: 0.7189 (t70) cc_final: 0.6849 (t0) REVERT: a 392 TYR cc_start: 0.7066 (m-80) cc_final: 0.6846 (m-80) outliers start: 80 outliers final: 66 residues processed: 458 average time/residue: 0.1253 time to fit residues: 86.9953 Evaluate side-chains 492 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 421 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 312 LEU Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 403 GLU Chi-restraints excluded: chain a residue 409 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 173 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 198 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS G 3 GLN c 373 HIS c 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.169403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140657 restraints weight = 28955.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.145406 restraints weight = 16289.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.148492 restraints weight = 10972.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.150692 restraints weight = 8328.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.151907 restraints weight = 6785.746| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17877 Z= 0.197 Angle : 0.721 18.315 24306 Z= 0.349 Chirality : 0.046 0.302 2781 Planarity : 0.005 0.059 3021 Dihedral : 4.937 24.422 2343 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.40 % Allowed : 18.73 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.18), residues: 2124 helix: -1.22 (0.28), residues: 312 sheet: 0.22 (0.21), residues: 687 loop : -1.04 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 13 TYR 0.023 0.002 TYR D 50 PHE 0.018 0.002 PHE a 261 TRP 0.058 0.002 TRP C 226 HIS 0.006 0.001 HIS E 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (17820) covalent geometry : angle 0.67954 / 0.34 (24162) SS BOND : bond 0.00511 / 0.29 ( 27) SS BOND : angle 1.40627 / 0.82 ( 54) hydrogen bonds : bond 0.04355 / 2.93 ( 593) hydrogen bonds : angle 6.15034 / 4.27 ( 1521) link_BETA1-4 : bond 0.00286 / 0.14 ( 4) link_BETA1-4 : angle 1.88098 / 1.06 ( 12) link_NAG-ASN : bond 0.00770 / 0.49 ( 26) link_NAG-ASN : angle 4.12724 / 2.48 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 421 time to evaluate : 0.589 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: C 133 MET cc_start: 0.7696 (mmm) cc_final: 0.6670 (tpt) REVERT: C 154 CYS cc_start: 0.3073 (OUTLIER) cc_final: 0.2611 (p) REVERT: D 83 ASP cc_start: 0.7451 (m-30) cc_final: 0.7026 (m-30) REVERT: D 107 GLU cc_start: 0.6520 (pt0) cc_final: 0.6083 (pt0) REVERT: E 80 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.6043 (pt) REVERT: E 83 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7632 (tp-100) REVERT: E 179 VAL cc_start: 0.8280 (p) cc_final: 0.7954 (m) REVERT: A 66 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6571 (tm-30) REVERT: A 68 GLN cc_start: 0.7565 (mt0) cc_final: 0.7022 (mt0) REVERT: A 133 MET cc_start: 0.7946 (tpp) cc_final: 0.7168 (tpp) REVERT: H 88 ARG cc_start: 0.7181 (mmm160) cc_final: 0.6830 (mmm160) REVERT: H 118 THR cc_start: 0.7400 (p) cc_final: 0.7197 (p) REVERT: H 211 LYS cc_start: 0.8331 (tppt) cc_final: 0.7877 (tppt) REVERT: B 236 SER cc_start: 0.7576 (t) cc_final: 0.7253 (m) REVERT: F 6 GLN cc_start: 0.6745 (mp10) cc_final: 0.6512 (mp10) REVERT: F 164 SER cc_start: 0.7836 (m) cc_final: 0.6884 (t) REVERT: G 118 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7665 (p) REVERT: c 299 LYS cc_start: 0.7568 (mtmm) cc_final: 0.7288 (mtmm) REVERT: b 320 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.6960 (mp10) REVERT: a 356 ASP cc_start: 0.7190 (t70) cc_final: 0.6841 (t0) outliers start: 84 outliers final: 71 residues processed: 458 average time/residue: 0.1305 time to fit residues: 91.0133 Evaluate side-chains 494 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 419 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 409 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 139 optimal weight: 0.0000 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS c 408 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.170218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139818 restraints weight = 29617.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.144970 restraints weight = 16172.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.148328 restraints weight = 10761.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.150605 restraints weight = 8121.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.152065 restraints weight = 6632.531| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17877 Z= 0.147 Angle : 0.713 18.276 24306 Z= 0.339 Chirality : 0.045 0.286 2781 Planarity : 0.005 0.063 3021 Dihedral : 4.807 24.208 2343 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.98 % Allowed : 19.36 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.19), residues: 2124 helix: -1.02 (0.29), residues: 312 sheet: 0.25 (0.21), residues: 687 loop : -0.98 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 13 TYR 0.023 0.001 TYR D 50 PHE 0.018 0.001 PHE a 261 TRP 0.047 0.002 TRP C 226 HIS 0.007 0.001 HIS E 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (17820) covalent geometry : angle 0.67155 / 0.33 (24162) SS BOND : bond 0.00451 / 0.25 ( 27) SS BOND : angle 1.31180 / 0.76 ( 54) hydrogen bonds : bond 0.03966 / 2.68 ( 593) hydrogen bonds : angle 6.02667 / 4.18 ( 1521) link_BETA1-4 : bond 0.00268 / 0.13 ( 4) link_BETA1-4 : angle 1.76921 / 0.99 ( 12) link_NAG-ASN : bond 0.00801 / 0.50 ( 26) link_NAG-ASN : angle 4.15382 / 2.49 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 427 time to evaluate : 0.600 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: C 77 LEU cc_start: 0.8336 (mt) cc_final: 0.8069 (mp) REVERT: C 133 MET cc_start: 0.7742 (mmm) cc_final: 0.6593 (tpt) REVERT: C 154 CYS cc_start: 0.3156 (OUTLIER) cc_final: 0.2642 (p) REVERT: C 222 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6978 (mm110) REVERT: D 83 ASP cc_start: 0.7412 (m-30) cc_final: 0.7055 (m-30) REVERT: D 107 GLU cc_start: 0.6625 (pt0) cc_final: 0.6145 (pt0) REVERT: E 80 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5979 (pt) REVERT: E 83 GLN cc_start: 0.7931 (tp-100) cc_final: 0.7698 (tp-100) REVERT: E 179 VAL cc_start: 0.8274 (p) cc_final: 0.7944 (m) REVERT: A 66 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6559 (tm-30) REVERT: A 68 GLN cc_start: 0.7529 (mt0) cc_final: 0.6961 (mt0) REVERT: A 133 MET cc_start: 0.7946 (tpp) cc_final: 0.7160 (tpp) REVERT: H 211 LYS cc_start: 0.8328 (tppt) cc_final: 0.7886 (tppt) REVERT: B 236 SER cc_start: 0.7703 (t) cc_final: 0.7384 (m) REVERT: F 6 GLN cc_start: 0.6460 (mp10) cc_final: 0.6252 (mp10) REVERT: F 164 SER cc_start: 0.7740 (m) cc_final: 0.6966 (t) REVERT: F 209 LYS cc_start: 0.7303 (mmtt) cc_final: 0.7061 (mmtm) REVERT: G 118 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7661 (p) REVERT: G 152 VAL cc_start: 0.8687 (m) cc_final: 0.8364 (p) REVERT: c 299 LYS cc_start: 0.7569 (mtmm) cc_final: 0.7289 (mtmm) REVERT: b 320 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6875 (mp10) REVERT: a 356 ASP cc_start: 0.7212 (t70) cc_final: 0.6807 (t0) outliers start: 76 outliers final: 68 residues processed: 460 average time/residue: 0.1263 time to fit residues: 87.8294 Evaluate side-chains 495 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 422 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 312 LEU Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 409 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 4 optimal weight: 0.0040 chunk 162 optimal weight: 0.4980 chunk 11 optimal weight: 0.0770 chunk 43 optimal weight: 0.9990 overall best weight: 0.3150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS c 408 ASN a 352 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.171056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.141688 restraints weight = 28831.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.146636 restraints weight = 15634.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.149989 restraints weight = 10344.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.152304 restraints weight = 7718.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.153693 restraints weight = 6228.565| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17877 Z= 0.141 Angle : 0.713 18.082 24306 Z= 0.338 Chirality : 0.045 0.283 2781 Planarity : 0.005 0.085 3021 Dihedral : 4.738 24.018 2343 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.66 % Allowed : 19.78 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.19), residues: 2124 helix: -0.93 (0.30), residues: 312 sheet: 0.28 (0.21), residues: 687 loop : -0.93 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG H 88 TYR 0.022 0.001 TYR D 50 PHE 0.018 0.001 PHE a 261 TRP 0.042 0.002 TRP C 226 HIS 0.009 0.001 HIS E 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (17820) covalent geometry : angle 0.67156 / 0.33 (24162) SS BOND : bond 0.00440 / 0.25 ( 27) SS BOND : angle 1.26727 / 0.73 ( 54) hydrogen bonds : bond 0.03867 / 2.60 ( 593) hydrogen bonds : angle 5.95349 / 4.13 ( 1521) link_BETA1-4 : bond 0.00345 / 0.17 ( 4) link_BETA1-4 : angle 1.73163 / 0.98 ( 12) link_NAG-ASN : bond 0.00798 / 0.50 ( 26) link_NAG-ASN : angle 4.11839 / 2.48 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 420 time to evaluate : 0.640 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: C 77 LEU cc_start: 0.8278 (mt) cc_final: 0.8027 (mp) REVERT: C 87 LYS cc_start: 0.6385 (mmmt) cc_final: 0.6007 (mmmt) REVERT: C 133 MET cc_start: 0.7739 (mmm) cc_final: 0.6554 (tpt) REVERT: C 154 CYS cc_start: 0.3188 (OUTLIER) cc_final: 0.2654 (p) REVERT: C 213 MET cc_start: 0.7635 (pmm) cc_final: 0.6974 (pmm) REVERT: C 222 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6990 (mm110) REVERT: D 83 ASP cc_start: 0.7394 (m-30) cc_final: 0.7029 (m-30) REVERT: D 107 GLU cc_start: 0.6639 (pt0) cc_final: 0.6183 (pt0) REVERT: E 80 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5951 (pt) REVERT: E 83 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7688 (tp-100) REVERT: E 179 VAL cc_start: 0.8270 (p) cc_final: 0.7937 (m) REVERT: A 66 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6547 (tm-30) REVERT: A 68 GLN cc_start: 0.7506 (mt0) cc_final: 0.6916 (mt0) REVERT: A 133 MET cc_start: 0.7920 (tpp) cc_final: 0.7110 (tpp) REVERT: H 83 GLN cc_start: 0.8079 (tp40) cc_final: 0.7830 (tp-100) REVERT: H 211 LYS cc_start: 0.8330 (tppt) cc_final: 0.7895 (tppt) REVERT: B 133 MET cc_start: 0.7502 (tpp) cc_final: 0.6404 (tpt) REVERT: B 236 SER cc_start: 0.7641 (t) cc_final: 0.7365 (m) REVERT: F 164 SER cc_start: 0.7717 (m) cc_final: 0.6827 (t) REVERT: F 209 LYS cc_start: 0.7293 (mmtt) cc_final: 0.7044 (mmtm) REVERT: G 118 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7655 (p) REVERT: G 152 VAL cc_start: 0.8708 (m) cc_final: 0.8374 (p) REVERT: c 299 LYS cc_start: 0.7572 (mtmm) cc_final: 0.7297 (mtmm) REVERT: c 413 MET cc_start: 0.7357 (tmm) cc_final: 0.7099 (tmm) REVERT: b 320 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6909 (mp10) REVERT: a 356 ASP cc_start: 0.7222 (t70) cc_final: 0.6868 (t70) outliers start: 70 outliers final: 64 residues processed: 451 average time/residue: 0.1354 time to fit residues: 92.2898 Evaluate side-chains 484 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 415 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 312 LEU Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 401 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 58 optimal weight: 0.4980 chunk 139 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 20 optimal weight: 0.0370 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 68 GLN A 157 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN H 102 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 HIS c 373 HIS c 408 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.170626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.142058 restraints weight = 29097.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.146822 restraints weight = 16238.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149971 restraints weight = 10899.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152049 restraints weight = 8213.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.153470 restraints weight = 6735.232| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17877 Z= 0.170 Angle : 0.726 18.003 24306 Z= 0.347 Chirality : 0.045 0.289 2781 Planarity : 0.005 0.078 3021 Dihedral : 4.799 23.907 2343 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.03 % Allowed : 19.94 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.19), residues: 2124 helix: -0.91 (0.30), residues: 312 sheet: 0.25 (0.21), residues: 687 loop : -0.96 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG H 88 TYR 0.022 0.001 TYR D 50 PHE 0.017 0.001 PHE a 261 TRP 0.038 0.002 TRP C 226 HIS 0.005 0.001 HIS G 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (17820) covalent geometry : angle 0.68560 / 0.34 (24162) SS BOND : bond 0.00486 / 0.27 ( 27) SS BOND : angle 1.35512 / 0.78 ( 54) hydrogen bonds : bond 0.04028 / 2.70 ( 593) hydrogen bonds : angle 5.98040 / 4.15 ( 1521) link_BETA1-4 : bond 0.00326 / 0.16 ( 4) link_BETA1-4 : angle 1.78646 / 1.01 ( 12) link_NAG-ASN : bond 0.00765 / 0.49 ( 26) link_NAG-ASN : angle 4.13079 / 2.49 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3493.13 seconds wall clock time: 61 minutes 8.18 seconds (3668.18 seconds total)