Starting phenix.real_space_refine on Tue Aug 26 06:19:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9avu_43923/08_2025/9avu_43923_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9avu_43923/08_2025/9avu_43923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9avu_43923/08_2025/9avu_43923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9avu_43923/08_2025/9avu_43923.map" model { file = "/net/cci-nas-00/data/ceres_data/9avu_43923/08_2025/9avu_43923_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9avu_43923/08_2025/9avu_43923_neut_trim.cif" } resolution = 2.45 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 83 5.16 5 C 11099 2.51 5 N 2698 2.21 5 O 3183 1.98 5 H 16600 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33665 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 6468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6468 Classifications: {'peptide': 399} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 378} Chain breaks: 1 Chain: "E" Number of atoms: 6627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 6627 Classifications: {'peptide': 408} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 381} Chain breaks: 2 Chain: "C" Number of atoms: 6468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6468 Classifications: {'peptide': 399} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 378} Chain breaks: 1 Chain: "D" Number of atoms: 6922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6922 Classifications: {'peptide': 427} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 396} Chain breaks: 1 Chain: "B" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 6623 Classifications: {'peptide': 413} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 386} Chain breaks: 1 Chain: "H" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N POV A 501 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV A 501 " occ=0.75 residue: pdb=" N POV E 601 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV E 601 " occ=0.75 Time building chain proxies: 5.32, per 1000 atoms: 0.16 Number of scatterers: 33665 At special positions: 0 Unit cell: (101.915, 110.33, 171.105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 83 16.00 P 2 15.00 O 3183 8.00 N 2698 7.00 C 11099 6.00 H 16600 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 162 " distance=2.04 Simple disulfide: pdb=" SG CYS E 152 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 137 " distance=2.04 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " 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 ALPHA1-2 " MAN H 5 " - " MAN H 6 " " MAN H 7 " - " MAN H 8 " " MAN H 9 " - " MAN H 10 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN K 4 " - " MAN K 5 " ALPHA1-3 " BMA H 3 " - " MAN H 9 " " MAN H 4 " - " MAN H 5 " " BMA J 3 " - " MAN J 8 " " MAN J 4 " - " MAN J 7 " " BMA K 3 " - " MAN K 4 " " MAN K 6 " - " MAN K 7 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " " MAN H 4 " - " MAN H 7 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG F 1 " - " ASN D 96 " " NAG H 1 " - " ASN A 161 " " NAG I 1 " - " ASN E 165 " " NAG J 1 " - " ASN C 161 " " NAG K 1 " - " ASN D 163 " " NAG L 1 " - " ASN B 163 " " NAG M 1 " - " ASN B 52 " Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 954.1 milliseconds Enol-peptide restraints added in 1.4 microseconds 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 19 sheets defined 43.8% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 Processing helix chain 'A' and resid 88 through 93 removed outlier: 4.004A pdb=" N GLY A 93 " --> pdb=" O ASP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.777A pdb=" N LYS A 104 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.515A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 249 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.535A pdb=" N SER A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 260 " --> pdb=" O THR A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 261 through 282 Processing helix chain 'A' and resid 292 through 320 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 389 through 456 removed outlier: 3.579A pdb=" N ALA A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 87 through 90 removed outlier: 3.887A pdb=" N SER E 90 " --> pdb=" O TYR E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 92 through 97 removed outlier: 4.051A pdb=" N GLU E 97 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 253 Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.502A pdb=" N PHE E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 270 Processing helix chain 'E' and resid 276 through 296 Processing helix chain 'E' and resid 307 through 335 Processing helix chain 'E' and resid 344 through 353 Processing helix chain 'E' and resid 354 through 360 removed outlier: 3.723A pdb=" N TYR E 358 " --> pdb=" O LYS E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 496 Processing helix chain 'C' and resid 22 through 32 removed outlier: 3.502A pdb=" N PHE C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 86 removed outlier: 4.154A pdb=" N LYS C 86 " --> pdb=" O TYR C 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 86' Processing helix chain 'C' and resid 88 through 93 removed outlier: 4.046A pdb=" N GLY C 93 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 231 through 238 Processing helix chain 'C' and resid 238 through 251 removed outlier: 3.940A pdb=" N GLY C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 260 removed outlier: 3.696A pdb=" N SER C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 260 " --> pdb=" O THR C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 260' Processing helix chain 'C' and resid 261 through 281 Processing helix chain 'C' and resid 292 through 320 removed outlier: 3.589A pdb=" N HIS C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 389 through 456 removed outlier: 3.530A pdb=" N PHE C 446 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ARG C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 34 Processing helix chain 'D' and resid 85 through 88 removed outlier: 3.873A pdb=" N GLN D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 88' Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.961A pdb=" N GLY D 95 " --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 107 No H-bonds generated for 'chain 'D' and resid 105 through 107' Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 262 through 269 removed outlier: 3.633A pdb=" N VAL D 266 " --> pdb=" O ILE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 296 removed outlier: 3.820A pdb=" N LYS D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 334 Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 352 through 359 removed outlier: 3.648A pdb=" N GLU D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 357 " --> pdb=" O THR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 433 Processing helix chain 'D' and resid 434 through 493 Proline residue: D 478 - end of helix Processing helix chain 'D' and resid 509 through 513 Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.985A pdb=" N GLY B 95 " --> pdb=" O ARG B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 248 through 261 removed outlier: 3.722A pdb=" N ALA B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 Processing helix chain 'B' and resid 272 through 294 removed outlier: 3.975A pdb=" N VAL B 276 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 331 Processing helix chain 'B' and resid 339 through 354 removed outlier: 4.132A pdb=" N LEU B 351 " --> pdb=" O PHE B 347 " (cutoff:3.500A) Proline residue: B 352 - end of helix Processing helix chain 'B' and resid 439 through 499 removed outlier: 3.691A pdb=" N LEU B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 481 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.172A pdb=" N HIS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.172A pdb=" N HIS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN A 73 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU A 60 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ARG A 75 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 58 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LYS A 77 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLN A 56 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLN A 79 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLY A 54 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N VAL A 81 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N THR A 52 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 112 removed outlier: 4.214A pdb=" N THR A 168 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU A 219 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR A 218 " --> pdb=" O TRP A 207 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TRP A 207 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP A 220 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS A 205 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR A 222 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY A 203 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS A 224 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER A 201 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 226 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 101 through 105 removed outlier: 3.959A pdb=" N SER E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 101 through 105 removed outlier: 3.959A pdb=" N SER E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU E 73 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU E 67 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER E 75 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR E 79 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU E 61 " --> pdb=" O TYR E 79 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP E 81 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU E 59 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLU E 83 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE E 57 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR E 85 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL E 55 " --> pdb=" O THR E 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 114 through 116 removed outlier: 6.854A pdb=" N ILE E 241 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 101 removed outlier: 4.241A pdb=" N HIS C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 101 removed outlier: 4.241A pdb=" N HIS C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE C 69 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL C 63 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR C 71 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG C 75 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU C 57 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS C 77 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU C 55 " --> pdb=" O LYS C 77 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN C 79 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL C 53 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N VAL C 81 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL C 51 " --> pdb=" O VAL C 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 112 removed outlier: 4.234A pdb=" N THR C 168 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU C 219 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR C 216 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TYR C 210 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU C 200 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN C 228 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE C 198 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 100 through 103 Processing sheet with id=AB3, first strand: chain 'D' and resid 100 through 103 removed outlier: 6.232A pdb=" N THR D 71 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU D 65 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR D 73 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP D 77 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU D 59 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU D 79 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU D 57 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLY D 81 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU D 55 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N THR D 83 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE D 53 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL D 51 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER D 181 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE D 53 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 112 through 114 removed outlier: 5.235A pdb=" N SER D 170 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN D 233 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE D 240 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 112 through 114 removed outlier: 5.235A pdb=" N SER D 170 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN D 233 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 184 through 187 Processing sheet with id=AB7, first strand: chain 'B' and resid 100 through 103 removed outlier: 4.647A pdb=" N GLY B 136 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 100 through 103 removed outlier: 4.647A pdb=" N GLY B 136 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA B 71 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU B 65 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR B 73 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP B 77 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU B 59 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLU B 79 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU B 57 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLN B 81 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU B 55 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N CYS B 83 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL B 53 " --> pdb=" O CYS B 83 " (cutoff:3.500A) removed outlier: 11.182A pdb=" N TYR B 85 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 13.509A pdb=" N VAL B 51 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 51 " --> pdb=" O ASN B 179 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLN B 181 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.761A pdb=" N SER B 170 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN B 229 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B 236 " --> pdb=" O ARG B 209 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.761A pdb=" N SER B 170 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN B 229 " --> pdb=" O SER B 170 " (cutoff:3.500A) 927 hydrogen bonds defined for protein. 2697 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.02 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 16572 1.04 - 1.24: 2117 1.24 - 1.44: 5362 1.44 - 1.64: 9912 1.64 - 1.84: 132 Bond restraints: 34095 Sorted by residual: bond pdb=" ND2 ASN B 52 " pdb="HD22 ASN B 52 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" ND2 ASN D 96 " pdb="HD22 ASN D 96 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" NZ LYS B 56 " pdb=" HZ3 LYS B 56 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS C 86 " pdb=" HZ2 LYS C 86 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS A 388 " pdb=" HZ1 LYS A 388 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 34090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.84: 61585 9.84 - 19.67: 2 19.67 - 29.51: 3 29.51 - 39.35: 1 39.35 - 49.19: 1 Bond angle restraints: 61592 Sorted by residual: angle pdb=" CA ILE A 387 " pdb=" N ILE A 387 " pdb=" H ILE A 387 " ideal model delta sigma weight residual 114.00 163.19 -49.19 3.00e+00 1.11e-01 2.69e+02 angle pdb=" CA GLY E 231 " pdb=" N GLY E 231 " pdb=" H GLY E 231 " ideal model delta sigma weight residual 114.00 149.35 -35.35 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CA GLN D 428 " pdb=" N GLN D 428 " pdb=" H GLN D 428 " ideal model delta sigma weight residual 114.00 143.41 -29.41 3.00e+00 1.11e-01 9.61e+01 angle pdb="HD21 ASN B 52 " pdb=" ND2 ASN B 52 " pdb="HD22 ASN B 52 " ideal model delta sigma weight residual 120.00 141.69 -21.69 3.00e+00 1.11e-01 5.23e+01 angle pdb=" N PHE A 345 " pdb=" CA PHE A 345 " pdb=" C PHE A 345 " ideal model delta sigma weight residual 113.01 104.43 8.58 1.20e+00 6.94e-01 5.11e+01 ... (remaining 61587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.78: 15781 25.78 - 51.57: 663 51.57 - 77.35: 159 77.35 - 103.14: 42 103.14 - 128.92: 8 Dihedral angle restraints: 16653 sinusoidal: 9342 harmonic: 7311 Sorted by residual: dihedral pdb=" C3 POV E 601 " pdb=" C31 POV E 601 " pdb=" O31 POV E 601 " pdb=" C32 POV E 601 " ideal model delta sinusoidal sigma weight residual 172.61 43.69 128.92 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" CA HIS C 320 " pdb=" C HIS C 320 " pdb=" N ARG C 321 " pdb=" CA ARG C 321 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CD ARG E 217 " pdb=" NE ARG E 217 " pdb=" CZ ARG E 217 " pdb=" NH1 ARG E 217 " ideal model delta sinusoidal sigma weight residual 0.00 -33.34 33.34 1 1.00e+01 1.00e-02 1.58e+01 ... (remaining 16650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 2859 0.256 - 0.513: 2 0.513 - 0.769: 0 0.769 - 1.025: 3 1.025 - 1.281: 2 Chirality restraints: 2866 Sorted by residual: chirality pdb=" C1 MAN H 4 " pdb=" O6 BMA H 3 " pdb=" C2 MAN H 4 " pdb=" O5 MAN H 4 " both_signs ideal model delta sigma weight residual False 2.40 2.18 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.83e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.45e+01 ... (remaining 2863 not shown) Planarity restraints: 4835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.312 2.00e-02 2.50e+03 2.67e-01 8.89e+02 pdb=" C7 NAG F 1 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.466 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " 0.299 2.00e-02 2.50e+03 2.53e-01 8.02e+02 pdb=" C7 NAG M 1 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.180 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " -0.438 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.239 2.00e-02 2.50e+03 2.06e-01 5.31e+02 pdb=" C7 NAG M 2 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.021 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.346 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.179 2.00e-02 2.50e+03 ... (remaining 4832 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 768 2.14 - 2.76: 61597 2.76 - 3.37: 95376 3.37 - 3.99: 128148 3.99 - 4.60: 197296 Nonbonded interactions: 483185 Sorted by model distance: nonbonded pdb="HD21 ASN C 161 " pdb=" O5 NAG J 1 " model vdw 1.528 1.960 nonbonded pdb=" HH TYR E 39 " pdb=" H TRP E 110 " model vdw 1.563 2.100 nonbonded pdb="HD21 ASN A 161 " pdb=" O5 NAG H 1 " model vdw 1.644 1.960 nonbonded pdb=" HE1 TRP B 108 " pdb=" HH TYR B 173 " model vdw 1.671 2.100 nonbonded pdb=" OE1 GLN B 169 " pdb=" HZ3 LYS B 230 " model vdw 1.688 2.450 ... (remaining 483180 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 21 through 456) selection = (chain 'C' and resid 21 through 456) } ncs_group { reference = chain 'F' selection = chain 'M' } ncs_group { reference = (chain 'H' and (resid 2 or resid 5 through 10)) selection = (chain 'J' and (resid 1 or resid 4 through 9)) } ncs_group { reference = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 29.610 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.007 0.324 17539 Z= 0.315 Angle : 0.928 20.985 23985 Z= 0.440 Chirality : 0.068 1.281 2866 Planarity : 0.013 0.267 2913 Dihedral : 16.603 128.923 6949 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.32 % Allowed : 11.80 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 0.94 (0.19), residues: 2024 helix: 2.13 (0.18), residues: 788 sheet: -0.37 (0.24), residues: 420 loop : -0.26 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 297 TYR 0.012 0.001 TYR A 297 PHE 0.038 0.002 PHE B 289 TRP 0.014 0.001 TRP A 331 HIS 0.022 0.002 HIS E 339 Details of bonding type rmsd covalent geometry : bond 0.00548 (17495) covalent geometry : angle 0.83138 (23859) SS BOND : bond 0.00666 ( 6) SS BOND : angle 1.77913 ( 12) hydrogen bonds : bond 0.10596 ( 843) hydrogen bonds : angle 5.17006 ( 2697) link_ALPHA1-2 : bond 0.00367 ( 6) link_ALPHA1-2 : angle 1.38742 ( 18) link_ALPHA1-3 : bond 0.00388 ( 6) link_ALPHA1-3 : angle 1.77248 ( 18) link_ALPHA1-6 : bond 0.00388 ( 7) link_ALPHA1-6 : angle 1.25848 ( 21) link_BETA1-4 : bond 0.02006 ( 12) link_BETA1-4 : angle 2.27444 ( 36) link_NAG-ASN : bond 0.18467 ( 7) link_NAG-ASN : angle 13.45822 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 339 HIS cc_start: 0.7366 (p-80) cc_final: 0.7020 (p90) REVERT: C 300 PHE cc_start: 0.7843 (t80) cc_final: 0.7566 (t80) REVERT: C 302 MET cc_start: 0.7659 (tpp) cc_final: 0.7391 (mmt) outliers start: 6 outliers final: 2 residues processed: 227 average time/residue: 0.9475 time to fit residues: 246.0438 Evaluate side-chains 207 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 345 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 339 HIS C 62 ASN D 116 ASN D 495 GLN B 176 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.141199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094528 restraints weight = 59375.705| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.22 r_work: 0.3125 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17539 Z= 0.128 Angle : 0.898 41.183 23985 Z= 0.367 Chirality : 0.048 0.486 2866 Planarity : 0.005 0.052 2913 Dihedral : 11.333 126.785 3006 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.01 % Allowed : 11.96 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 1.31 (0.19), residues: 2024 helix: 2.63 (0.18), residues: 788 sheet: -0.33 (0.24), residues: 421 loop : -0.17 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 217 TYR 0.010 0.001 TYR B 244 PHE 0.029 0.001 PHE A 345 TRP 0.009 0.001 TRP C 80 HIS 0.007 0.001 HIS C 428 Details of bonding type rmsd covalent geometry : bond 0.00276 (17495) covalent geometry : angle 0.57234 (23859) SS BOND : bond 0.01977 ( 6) SS BOND : angle 1.51738 ( 12) hydrogen bonds : bond 0.04507 ( 843) hydrogen bonds : angle 4.25747 ( 2697) link_ALPHA1-2 : bond 0.00359 ( 6) link_ALPHA1-2 : angle 1.55869 ( 18) link_ALPHA1-3 : bond 0.00572 ( 6) link_ALPHA1-3 : angle 1.96208 ( 18) link_ALPHA1-6 : bond 0.00703 ( 7) link_ALPHA1-6 : angle 1.74763 ( 21) link_BETA1-4 : bond 0.00420 ( 12) link_BETA1-4 : angle 2.19717 ( 36) link_NAG-ASN : bond 0.00568 ( 7) link_NAG-ASN : angle 23.03359 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 PHE cc_start: 0.7780 (t80) cc_final: 0.7528 (t80) REVERT: C 302 MET cc_start: 0.7691 (tpp) cc_final: 0.7416 (mmt) REVERT: D 307 LEU cc_start: 0.8424 (tp) cc_final: 0.8136 (tt) outliers start: 19 outliers final: 6 residues processed: 219 average time/residue: 0.9503 time to fit residues: 239.2834 Evaluate side-chains 208 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 202 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 309 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 198 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 137 optimal weight: 0.0980 chunk 143 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 GLN D 116 ASN D 495 GLN B 176 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.138708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091941 restraints weight = 58898.184| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.18 r_work: 0.3084 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 17539 Z= 0.181 Angle : 0.892 40.757 23985 Z= 0.365 Chirality : 0.048 0.483 2866 Planarity : 0.005 0.047 2913 Dihedral : 10.434 125.508 3001 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.07 % Allowed : 12.07 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 1.48 (0.19), residues: 2024 helix: 2.80 (0.18), residues: 785 sheet: -0.25 (0.24), residues: 429 loop : -0.09 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 101 TYR 0.010 0.001 TYR B 244 PHE 0.013 0.001 PHE A 345 TRP 0.010 0.001 TRP B 192 HIS 0.004 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00422 (17495) covalent geometry : angle 0.56244 (23859) SS BOND : bond 0.01159 ( 6) SS BOND : angle 1.87582 ( 12) hydrogen bonds : bond 0.04406 ( 843) hydrogen bonds : angle 4.08196 ( 2697) link_ALPHA1-2 : bond 0.00343 ( 6) link_ALPHA1-2 : angle 1.61110 ( 18) link_ALPHA1-3 : bond 0.00586 ( 6) link_ALPHA1-3 : angle 1.76816 ( 18) link_ALPHA1-6 : bond 0.00745 ( 7) link_ALPHA1-6 : angle 1.85956 ( 21) link_BETA1-4 : bond 0.00403 ( 12) link_BETA1-4 : angle 2.26498 ( 36) link_NAG-ASN : bond 0.00390 ( 7) link_NAG-ASN : angle 23.03206 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 349 GLN cc_start: 0.7189 (mt0) cc_final: 0.6973 (mt0) REVERT: C 300 PHE cc_start: 0.7875 (t80) cc_final: 0.7601 (t80) REVERT: B 256 SER cc_start: 0.8583 (m) cc_final: 0.8144 (p) outliers start: 20 outliers final: 9 residues processed: 220 average time/residue: 0.9856 time to fit residues: 248.9000 Evaluate side-chains 213 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 309 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 99 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 91 optimal weight: 0.0980 chunk 195 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 173 optimal weight: 0.2980 chunk 108 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN D 495 GLN B 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.138375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091325 restraints weight = 58671.432| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.20 r_work: 0.3088 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17539 Z= 0.137 Angle : 0.885 42.054 23985 Z= 0.356 Chirality : 0.046 0.420 2866 Planarity : 0.004 0.043 2913 Dihedral : 9.410 123.431 3001 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.07 % Allowed : 12.71 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 1.58 (0.19), residues: 2024 helix: 2.93 (0.18), residues: 783 sheet: -0.13 (0.24), residues: 418 loop : -0.13 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 297 TYR 0.011 0.001 TYR B 139 PHE 0.016 0.001 PHE B 289 TRP 0.008 0.001 TRP C 80 HIS 0.003 0.001 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00306 (17495) covalent geometry : angle 0.53502 (23859) SS BOND : bond 0.01529 ( 6) SS BOND : angle 1.97914 ( 12) hydrogen bonds : bond 0.04113 ( 843) hydrogen bonds : angle 3.94104 ( 2697) link_ALPHA1-2 : bond 0.00364 ( 6) link_ALPHA1-2 : angle 1.54864 ( 18) link_ALPHA1-3 : bond 0.00649 ( 6) link_ALPHA1-3 : angle 1.70735 ( 18) link_ALPHA1-6 : bond 0.00697 ( 7) link_ALPHA1-6 : angle 1.78001 ( 21) link_BETA1-4 : bond 0.00304 ( 12) link_BETA1-4 : angle 2.04584 ( 36) link_NAG-ASN : bond 0.00362 ( 7) link_NAG-ASN : angle 23.50802 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 PHE cc_start: 0.7849 (t80) cc_final: 0.7619 (t80) REVERT: C 314 ILE cc_start: 0.7980 (mm) cc_final: 0.7744 (mt) REVERT: B 256 SER cc_start: 0.8590 (m) cc_final: 0.8173 (p) outliers start: 20 outliers final: 13 residues processed: 215 average time/residue: 0.9411 time to fit residues: 232.1333 Evaluate side-chains 215 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 490 GLN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 337 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 42 optimal weight: 0.9980 chunk 121 optimal weight: 0.1980 chunk 101 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN D 495 GLN B 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.137337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090157 restraints weight = 59121.725| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.20 r_work: 0.3076 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17539 Z= 0.170 Angle : 0.888 42.300 23985 Z= 0.359 Chirality : 0.047 0.465 2866 Planarity : 0.004 0.042 2913 Dihedral : 8.999 121.846 3001 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.12 % Allowed : 12.65 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 1.60 (0.19), residues: 2024 helix: 2.94 (0.18), residues: 784 sheet: -0.05 (0.25), residues: 412 loop : -0.15 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 297 TYR 0.010 0.001 TYR B 127 PHE 0.013 0.001 PHE E 36 TRP 0.009 0.001 TRP B 192 HIS 0.004 0.001 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00390 (17495) covalent geometry : angle 0.54421 (23859) SS BOND : bond 0.01673 ( 6) SS BOND : angle 2.07764 ( 12) hydrogen bonds : bond 0.04216 ( 843) hydrogen bonds : angle 3.91029 ( 2697) link_ALPHA1-2 : bond 0.00310 ( 6) link_ALPHA1-2 : angle 1.60987 ( 18) link_ALPHA1-3 : bond 0.00576 ( 6) link_ALPHA1-3 : angle 1.73817 ( 18) link_ALPHA1-6 : bond 0.00804 ( 7) link_ALPHA1-6 : angle 1.83155 ( 21) link_BETA1-4 : bond 0.00351 ( 12) link_BETA1-4 : angle 2.15314 ( 36) link_NAG-ASN : bond 0.00305 ( 7) link_NAG-ASN : angle 23.35694 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 PHE cc_start: 0.7933 (t80) cc_final: 0.7703 (t80) REVERT: C 314 ILE cc_start: 0.8003 (mm) cc_final: 0.7769 (mt) REVERT: D 287 GLN cc_start: 0.8349 (mt0) cc_final: 0.8111 (mt0) REVERT: B 256 SER cc_start: 0.8666 (m) cc_final: 0.8268 (p) REVERT: B 339 MET cc_start: 0.3233 (tpp) cc_final: 0.2953 (mmt) outliers start: 21 outliers final: 15 residues processed: 217 average time/residue: 0.9301 time to fit residues: 233.0300 Evaluate side-chains 215 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 490 GLN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 68 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN D 331 ASN D 495 GLN B 176 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089661 restraints weight = 58886.451| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.20 r_work: 0.3069 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 17539 Z= 0.185 Angle : 0.890 42.466 23985 Z= 0.361 Chirality : 0.047 0.477 2866 Planarity : 0.005 0.044 2913 Dihedral : 8.811 120.257 3001 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.33 % Allowed : 12.60 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 1.62 (0.19), residues: 2024 helix: 2.95 (0.18), residues: 783 sheet: -0.03 (0.25), residues: 416 loop : -0.15 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 297 TYR 0.011 0.001 TYR B 127 PHE 0.016 0.001 PHE B 289 TRP 0.009 0.001 TRP B 192 HIS 0.004 0.001 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00430 (17495) covalent geometry : angle 0.54579 (23859) SS BOND : bond 0.01728 ( 6) SS BOND : angle 3.07470 ( 12) hydrogen bonds : bond 0.04257 ( 843) hydrogen bonds : angle 3.89604 ( 2697) link_ALPHA1-2 : bond 0.00295 ( 6) link_ALPHA1-2 : angle 1.62390 ( 18) link_ALPHA1-3 : bond 0.00589 ( 6) link_ALPHA1-3 : angle 1.69090 ( 18) link_ALPHA1-6 : bond 0.00769 ( 7) link_ALPHA1-6 : angle 1.84722 ( 21) link_BETA1-4 : bond 0.00372 ( 12) link_BETA1-4 : angle 2.14005 ( 36) link_NAG-ASN : bond 0.00258 ( 7) link_NAG-ASN : angle 23.32567 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 PHE cc_start: 0.7963 (t80) cc_final: 0.7712 (t80) REVERT: C 314 ILE cc_start: 0.7974 (mm) cc_final: 0.7741 (mt) REVERT: C 349 MET cc_start: 0.4718 (tpt) cc_final: 0.4285 (tpt) REVERT: B 215 MET cc_start: 0.8563 (tmm) cc_final: 0.8341 (tmm) REVERT: B 256 SER cc_start: 0.8681 (m) cc_final: 0.8307 (p) outliers start: 25 outliers final: 19 residues processed: 224 average time/residue: 0.8616 time to fit residues: 223.5646 Evaluate side-chains 222 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 490 GLN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 179 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 158 optimal weight: 0.0060 chunk 95 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 56 optimal weight: 0.0970 chunk 139 optimal weight: 0.9980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN D 495 GLN B 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.137599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.090488 restraints weight = 59007.120| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.20 r_work: 0.3077 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17539 Z= 0.138 Angle : 0.879 42.783 23985 Z= 0.353 Chirality : 0.046 0.434 2866 Planarity : 0.004 0.045 2913 Dihedral : 8.492 116.003 3001 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.12 % Allowed : 13.19 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 1.68 (0.19), residues: 2024 helix: 3.05 (0.18), residues: 783 sheet: -0.11 (0.24), residues: 426 loop : -0.09 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 297 TYR 0.011 0.001 TYR B 139 PHE 0.016 0.001 PHE B 289 TRP 0.008 0.001 TRP C 80 HIS 0.003 0.001 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00312 (17495) covalent geometry : angle 0.52076 (23859) SS BOND : bond 0.02311 ( 6) SS BOND : angle 2.32383 ( 12) hydrogen bonds : bond 0.04030 ( 843) hydrogen bonds : angle 3.82956 ( 2697) link_ALPHA1-2 : bond 0.00321 ( 6) link_ALPHA1-2 : angle 1.56902 ( 18) link_ALPHA1-3 : bond 0.00626 ( 6) link_ALPHA1-3 : angle 1.65145 ( 18) link_ALPHA1-6 : bond 0.00805 ( 7) link_ALPHA1-6 : angle 1.86509 ( 21) link_BETA1-4 : bond 0.00321 ( 12) link_BETA1-4 : angle 1.99724 ( 36) link_NAG-ASN : bond 0.00334 ( 7) link_NAG-ASN : angle 23.58557 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 349 GLN cc_start: 0.7164 (mt0) cc_final: 0.6916 (mp10) REVERT: C 300 PHE cc_start: 0.7968 (t80) cc_final: 0.7738 (t80) REVERT: C 314 ILE cc_start: 0.7969 (mm) cc_final: 0.7739 (mt) REVERT: C 349 MET cc_start: 0.4712 (tpt) cc_final: 0.4360 (tpt) REVERT: B 256 SER cc_start: 0.8668 (m) cc_final: 0.8310 (p) REVERT: B 339 MET cc_start: 0.3418 (tpp) cc_final: 0.3102 (mmt) outliers start: 21 outliers final: 20 residues processed: 216 average time/residue: 0.9183 time to fit residues: 229.7584 Evaluate side-chains 221 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 490 GLN Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 81 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 172 optimal weight: 0.1980 chunk 151 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 200 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN D 231 ASN D 495 GLN B 176 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.090812 restraints weight = 58677.732| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.21 r_work: 0.3083 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17539 Z= 0.127 Angle : 0.877 42.904 23985 Z= 0.350 Chirality : 0.045 0.431 2866 Planarity : 0.004 0.048 2913 Dihedral : 8.230 110.800 3001 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.28 % Allowed : 13.08 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 1.74 (0.19), residues: 2024 helix: 3.12 (0.18), residues: 783 sheet: -0.10 (0.24), residues: 425 loop : -0.07 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 297 TYR 0.011 0.001 TYR B 139 PHE 0.011 0.001 PHE E 36 TRP 0.008 0.001 TRP C 80 HIS 0.004 0.001 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00287 (17495) covalent geometry : angle 0.51455 (23859) SS BOND : bond 0.01768 ( 6) SS BOND : angle 2.22081 ( 12) hydrogen bonds : bond 0.03919 ( 843) hydrogen bonds : angle 3.77740 ( 2697) link_ALPHA1-2 : bond 0.00311 ( 6) link_ALPHA1-2 : angle 1.57702 ( 18) link_ALPHA1-3 : bond 0.00633 ( 6) link_ALPHA1-3 : angle 1.64767 ( 18) link_ALPHA1-6 : bond 0.00818 ( 7) link_ALPHA1-6 : angle 1.89860 ( 21) link_BETA1-4 : bond 0.00313 ( 12) link_BETA1-4 : angle 1.92716 ( 36) link_NAG-ASN : bond 0.00349 ( 7) link_NAG-ASN : angle 23.67571 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 PHE cc_start: 0.7968 (t80) cc_final: 0.7744 (t80) REVERT: C 314 ILE cc_start: 0.8011 (mm) cc_final: 0.7784 (mt) REVERT: C 349 MET cc_start: 0.4742 (tpt) cc_final: 0.4410 (tpt) REVERT: B 256 SER cc_start: 0.8683 (m) cc_final: 0.8328 (p) REVERT: B 293 LYS cc_start: 0.8255 (mtpt) cc_final: 0.8011 (mtpp) REVERT: B 339 MET cc_start: 0.3358 (tpp) cc_final: 0.3056 (mmt) outliers start: 24 outliers final: 19 residues processed: 214 average time/residue: 0.9333 time to fit residues: 230.0714 Evaluate side-chains 217 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 490 GLN Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 154 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 170 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN D 495 GLN B 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090162 restraints weight = 58688.128| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.20 r_work: 0.3071 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17539 Z= 0.160 Angle : 0.879 42.786 23985 Z= 0.354 Chirality : 0.046 0.469 2866 Planarity : 0.004 0.050 2913 Dihedral : 8.231 106.850 3001 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.07 % Allowed : 13.24 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 1.71 (0.19), residues: 2024 helix: 3.08 (0.18), residues: 784 sheet: -0.08 (0.24), residues: 426 loop : -0.09 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 297 TYR 0.010 0.001 TYR B 127 PHE 0.019 0.001 PHE B 289 TRP 0.008 0.001 TRP B 192 HIS 0.003 0.001 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00368 (17495) covalent geometry : angle 0.52480 (23859) SS BOND : bond 0.01661 ( 6) SS BOND : angle 2.44293 ( 12) hydrogen bonds : bond 0.04036 ( 843) hydrogen bonds : angle 3.79789 ( 2697) link_ALPHA1-2 : bond 0.00272 ( 6) link_ALPHA1-2 : angle 1.63716 ( 18) link_ALPHA1-3 : bond 0.00578 ( 6) link_ALPHA1-3 : angle 1.65017 ( 18) link_ALPHA1-6 : bond 0.00741 ( 7) link_ALPHA1-6 : angle 1.93729 ( 21) link_BETA1-4 : bond 0.00357 ( 12) link_BETA1-4 : angle 2.00511 ( 36) link_NAG-ASN : bond 0.00277 ( 7) link_NAG-ASN : angle 23.47441 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 PHE cc_start: 0.7944 (t80) cc_final: 0.7742 (t80) REVERT: C 349 MET cc_start: 0.4878 (tpt) cc_final: 0.4643 (tpt) REVERT: B 256 SER cc_start: 0.8701 (m) cc_final: 0.8355 (p) REVERT: B 339 MET cc_start: 0.3274 (tpp) cc_final: 0.2946 (mmt) outliers start: 20 outliers final: 19 residues processed: 214 average time/residue: 0.9498 time to fit residues: 234.3535 Evaluate side-chains 220 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 490 GLN Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 160 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 127 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN D 495 GLN B 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.090243 restraints weight = 59111.809| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.22 r_work: 0.3072 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17539 Z= 0.146 Angle : 0.879 42.768 23985 Z= 0.353 Chirality : 0.046 0.448 2866 Planarity : 0.004 0.052 2913 Dihedral : 8.120 103.209 3001 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.12 % Allowed : 13.35 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 1.75 (0.19), residues: 2024 helix: 3.13 (0.18), residues: 783 sheet: -0.06 (0.24), residues: 422 loop : -0.10 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 297 TYR 0.013 0.001 TYR B 139 PHE 0.016 0.001 PHE B 289 TRP 0.008 0.001 TRP C 80 HIS 0.003 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00332 (17495) covalent geometry : angle 0.52208 (23859) SS BOND : bond 0.01956 ( 6) SS BOND : angle 2.27525 ( 12) hydrogen bonds : bond 0.03969 ( 843) hydrogen bonds : angle 3.79312 ( 2697) link_ALPHA1-2 : bond 0.00288 ( 6) link_ALPHA1-2 : angle 1.61061 ( 18) link_ALPHA1-3 : bond 0.00592 ( 6) link_ALPHA1-3 : angle 1.60572 ( 18) link_ALPHA1-6 : bond 0.00731 ( 7) link_ALPHA1-6 : angle 1.95809 ( 21) link_BETA1-4 : bond 0.00340 ( 12) link_BETA1-4 : angle 1.97062 ( 36) link_NAG-ASN : bond 0.00308 ( 7) link_NAG-ASN : angle 23.54087 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 PHE cc_start: 0.7943 (t80) cc_final: 0.7735 (t80) REVERT: C 349 MET cc_start: 0.4959 (tpt) cc_final: 0.4689 (tpt) REVERT: B 256 SER cc_start: 0.8697 (m) cc_final: 0.8351 (p) REVERT: B 339 MET cc_start: 0.3241 (tpp) cc_final: 0.2920 (mmt) outliers start: 21 outliers final: 20 residues processed: 219 average time/residue: 0.9005 time to fit residues: 227.4856 Evaluate side-chains 226 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 490 GLN Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 184 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 178 optimal weight: 0.5980 chunk 119 optimal weight: 0.1980 chunk 47 optimal weight: 0.5980 chunk 193 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN D 495 GLN B 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.138600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091630 restraints weight = 58756.062| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.21 r_work: 0.3096 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17539 Z= 0.108 Angle : 0.872 42.962 23985 Z= 0.346 Chirality : 0.045 0.401 2866 Planarity : 0.004 0.050 2913 Dihedral : 7.749 98.350 3001 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.96 % Allowed : 13.61 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 1.83 (0.19), residues: 2024 helix: 3.22 (0.18), residues: 784 sheet: -0.08 (0.24), residues: 425 loop : -0.03 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 297 TYR 0.011 0.001 TYR B 139 PHE 0.017 0.001 PHE B 289 TRP 0.009 0.001 TRP C 80 HIS 0.003 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00240 (17495) covalent geometry : angle 0.50054 (23859) SS BOND : bond 0.01842 ( 6) SS BOND : angle 2.21663 ( 12) hydrogen bonds : bond 0.03746 ( 843) hydrogen bonds : angle 3.69842 ( 2697) link_ALPHA1-2 : bond 0.00328 ( 6) link_ALPHA1-2 : angle 1.54909 ( 18) link_ALPHA1-3 : bond 0.00642 ( 6) link_ALPHA1-3 : angle 1.61074 ( 18) link_ALPHA1-6 : bond 0.00769 ( 7) link_ALPHA1-6 : angle 1.91039 ( 21) link_BETA1-4 : bond 0.00291 ( 12) link_BETA1-4 : angle 1.82379 ( 36) link_NAG-ASN : bond 0.00425 ( 7) link_NAG-ASN : angle 23.82898 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12585.29 seconds wall clock time: 212 minutes 56.88 seconds (12776.88 seconds total)