Starting phenix.real_space_refine on Sun Jun 29 07:46:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9avu_43923/06_2025/9avu_43923_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9avu_43923/06_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_43923/06_2025/9avu_43923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9avu_43923/06_2025/9avu_43923.map" model { file = "/net/cci-nas-00/data/ceres_data/9avu_43923/06_2025/9avu_43923_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9avu_43923/06_2025/9avu_43923_neut_trim.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.68, per 1000 atoms: 0.53 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: 9.13 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.69 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: 13.25 Time building geometry restraints manager: 11.11 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: 14.020 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: 0.540 Extract box with map and model: 1.300 Check model and map are aligned: 0.210 Set scattering table: 0.300 Process input model: 72.040 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.014 0.001 TRP A 331 HIS 0.022 0.002 HIS E 339 PHE 0.038 0.002 PHE B 289 TYR 0.012 0.001 TYR A 297 ARG 0.014 0.001 ARG D 297 Details of bonding type rmsd link_NAG-ASN : bond 0.18467 ( 7) link_NAG-ASN : angle 13.45822 ( 21) 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_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) hydrogen bonds : bond 0.10596 ( 843) hydrogen bonds : angle 5.17006 ( 2697) SS BOND : bond 0.00666 ( 6) SS BOND : angle 1.77913 ( 12) covalent geometry : bond 0.00548 (17495) covalent geometry : angle 0.83138 (23859) *********************** 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 : 2.773 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: 2.1938 time to fit residues: 576.4469 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 : 2.680 ------------------------------------------------------------------------------- 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 169 optimal weight: 0.5980 chunk 152 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 81 optimal weight: 0.1980 chunk 157 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.140288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.093666 restraints weight = 59003.800| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.20 r_work: 0.3113 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17539 Z= 0.147 Angle : 0.898 40.501 23985 Z= 0.370 Chirality : 0.048 0.507 2866 Planarity : 0.005 0.052 2913 Dihedral : 11.420 127.560 3006 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.96 % Allowed : 11.96 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 2024 helix: 2.60 (0.18), residues: 788 sheet: -0.32 (0.24), residues: 421 loop : -0.17 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 80 HIS 0.007 0.001 HIS C 428 PHE 0.029 0.001 PHE A 345 TYR 0.010 0.001 TYR B 244 ARG 0.005 0.000 ARG E 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 7) link_NAG-ASN : angle 22.80504 ( 21) link_ALPHA1-6 : bond 0.00688 ( 7) link_ALPHA1-6 : angle 1.74993 ( 21) link_BETA1-4 : bond 0.00504 ( 12) link_BETA1-4 : angle 2.19608 ( 36) link_ALPHA1-2 : bond 0.00343 ( 6) link_ALPHA1-2 : angle 1.61477 ( 18) link_ALPHA1-3 : bond 0.00555 ( 6) link_ALPHA1-3 : angle 1.91269 ( 18) hydrogen bonds : bond 0.04648 ( 843) hydrogen bonds : angle 4.27094 ( 2697) SS BOND : bond 0.01825 ( 6) SS BOND : angle 1.86718 ( 12) covalent geometry : bond 0.00319 (17495) covalent geometry : angle 0.58039 (23859) *********************** 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 230 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 PHE cc_start: 0.7767 (t80) cc_final: 0.7479 (t80) REVERT: C 302 MET cc_start: 0.7697 (tpp) cc_final: 0.7415 (mmt) REVERT: D 307 LEU cc_start: 0.8432 (tp) cc_final: 0.8143 (tt) outliers start: 18 outliers final: 6 residues processed: 221 average time/residue: 2.1383 time to fit residues: 547.0700 Evaluate side-chains 209 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 203 time to evaluate : 2.721 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.9990 chunk 184 optimal weight: 0.0270 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 176 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.137908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.090875 restraints weight = 58839.190| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.20 r_work: 0.3081 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 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 = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17539 Z= 0.157 Angle : 0.887 41.152 23985 Z= 0.360 Chirality : 0.047 0.449 2866 Planarity : 0.005 0.046 2913 Dihedral : 10.122 124.981 3001 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.01 % Allowed : 12.07 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2024 helix: 2.83 (0.18), residues: 783 sheet: -0.23 (0.24), residues: 428 loop : -0.12 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 192 HIS 0.004 0.001 HIS B 498 PHE 0.016 0.001 PHE A 345 TYR 0.010 0.001 TYR B 139 ARG 0.005 0.000 ARG D 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 7) link_NAG-ASN : angle 23.13488 ( 21) link_ALPHA1-6 : bond 0.00785 ( 7) link_ALPHA1-6 : angle 1.83153 ( 21) link_BETA1-4 : bond 0.00347 ( 12) link_BETA1-4 : angle 2.19169 ( 36) link_ALPHA1-2 : bond 0.00358 ( 6) link_ALPHA1-2 : angle 1.54695 ( 18) link_ALPHA1-3 : bond 0.00622 ( 6) link_ALPHA1-3 : angle 1.67178 ( 18) hydrogen bonds : bond 0.04290 ( 843) hydrogen bonds : angle 4.02873 ( 2697) SS BOND : bond 0.01415 ( 6) SS BOND : angle 2.10074 ( 12) covalent geometry : bond 0.00360 (17495) covalent geometry : angle 0.55043 (23859) *********************** 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 231 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 349 GLN cc_start: 0.7161 (mt0) cc_final: 0.6947 (mt0) REVERT: C 300 PHE cc_start: 0.7869 (t80) cc_final: 0.7620 (t80) REVERT: C 314 ILE cc_start: 0.8027 (mm) cc_final: 0.7788 (mt) REVERT: D 466 ARG cc_start: 0.6986 (mtp180) cc_final: 0.6756 (mtp180) REVERT: B 256 SER cc_start: 0.8573 (m) cc_final: 0.8134 (p) outliers start: 19 outliers final: 8 residues processed: 219 average time/residue: 2.1122 time to fit residues: 536.4544 Evaluate side-chains 213 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 205 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP 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 490 GLN 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 109 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.137890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.090744 restraints weight = 58958.097| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.21 r_work: 0.3080 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 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 = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17539 Z= 0.159 Angle : 0.886 42.072 23985 Z= 0.357 Chirality : 0.046 0.448 2866 Planarity : 0.004 0.043 2913 Dihedral : 9.288 123.968 3001 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.96 % Allowed : 12.55 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.19), residues: 2024 helix: 2.90 (0.18), residues: 784 sheet: -0.08 (0.25), residues: 413 loop : -0.14 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 192 HIS 0.003 0.001 HIS B 498 PHE 0.015 0.001 PHE B 289 TYR 0.010 0.001 TYR B 139 ARG 0.005 0.000 ARG D 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 7) link_NAG-ASN : angle 23.39334 ( 21) link_ALPHA1-6 : bond 0.00773 ( 7) link_ALPHA1-6 : angle 1.81222 ( 21) link_BETA1-4 : bond 0.00329 ( 12) link_BETA1-4 : angle 2.13429 ( 36) link_ALPHA1-2 : bond 0.00322 ( 6) link_ALPHA1-2 : angle 1.58960 ( 18) link_ALPHA1-3 : bond 0.00609 ( 6) link_ALPHA1-3 : angle 1.74854 ( 18) hydrogen bonds : bond 0.04183 ( 843) hydrogen bonds : angle 3.94289 ( 2697) SS BOND : bond 0.01664 ( 6) SS BOND : angle 1.80120 ( 12) covalent geometry : bond 0.00362 (17495) covalent geometry : angle 0.53990 (23859) *********************** 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 224 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 PHE cc_start: 0.7892 (t80) cc_final: 0.7660 (t80) REVERT: C 314 ILE cc_start: 0.8007 (mm) cc_final: 0.7771 (mt) REVERT: D 287 GLN cc_start: 0.8268 (mt0) cc_final: 0.8039 (mt0) REVERT: B 256 SER cc_start: 0.8605 (m) cc_final: 0.8195 (p) outliers start: 18 outliers final: 11 residues processed: 214 average time/residue: 2.6312 time to fit residues: 660.5968 Evaluate side-chains 211 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 4.235 ------------------------------------------------------------------------------- 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 25 THR Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain B residue 46 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 176 optimal weight: 0.3980 chunk 2 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.138036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.090960 restraints weight = 58845.274| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.20 r_work: 0.3087 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: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17539 Z= 0.135 Angle : 0.879 42.506 23985 Z= 0.352 Chirality : 0.046 0.430 2866 Planarity : 0.004 0.043 2913 Dihedral : 8.798 120.411 3001 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.07 % Allowed : 12.39 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.19), residues: 2024 helix: 3.01 (0.18), residues: 784 sheet: -0.06 (0.25), residues: 414 loop : -0.11 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 80 HIS 0.004 0.001 HIS B 498 PHE 0.011 0.001 PHE E 36 TYR 0.011 0.001 TYR B 139 ARG 0.005 0.000 ARG D 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 7) link_NAG-ASN : angle 23.54016 ( 21) link_ALPHA1-6 : bond 0.00834 ( 7) link_ALPHA1-6 : angle 1.83997 ( 21) link_BETA1-4 : bond 0.00302 ( 12) link_BETA1-4 : angle 2.01573 ( 36) link_ALPHA1-2 : bond 0.00336 ( 6) link_ALPHA1-2 : angle 1.53447 ( 18) link_ALPHA1-3 : bond 0.00647 ( 6) link_ALPHA1-3 : angle 1.70243 ( 18) hydrogen bonds : bond 0.04037 ( 843) hydrogen bonds : angle 3.85638 ( 2697) SS BOND : bond 0.01947 ( 6) SS BOND : angle 1.98967 ( 12) covalent geometry : bond 0.00304 (17495) covalent geometry : angle 0.52338 (23859) *********************** 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 227 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 3.398 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: 0.7930 (t80) cc_final: 0.7706 (t80) REVERT: C 314 ILE cc_start: 0.8017 (mm) cc_final: 0.7788 (mt) REVERT: C 349 MET cc_start: 0.4572 (tpt) cc_final: 0.4185 (tpt) REVERT: D 287 GLN cc_start: 0.8265 (mt0) cc_final: 0.8044 (mt0) REVERT: B 256 SER cc_start: 0.8660 (m) cc_final: 0.8266 (p) REVERT: B 339 MET cc_start: 0.3364 (tpp) cc_final: 0.3067 (mmt) outliers start: 20 outliers final: 15 residues processed: 216 average time/residue: 2.1741 time to fit residues: 547.0561 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 : 2.498 ------------------------------------------------------------------------------- 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 162 CYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 438 CYS Chi-restraints excluded: chain D residue 490 GLN Chi-restraints excluded: chain B residue 46 HIS 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 65 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 450 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 = 0.3745 r_free = 0.3745 target = 0.137469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090245 restraints weight = 58889.451| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.20 r_work: 0.3072 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 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 = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17539 Z= 0.160 Angle : 0.884 42.665 23985 Z= 0.356 Chirality : 0.046 0.460 2866 Planarity : 0.004 0.043 2913 Dihedral : 8.606 117.340 3001 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.12 % Allowed : 12.76 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 2024 helix: 3.03 (0.18), residues: 784 sheet: -0.05 (0.25), residues: 420 loop : -0.10 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 192 HIS 0.003 0.001 HIS C 45 PHE 0.018 0.001 PHE B 289 TYR 0.009 0.001 TYR B 127 ARG 0.006 0.000 ARG D 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 7) link_NAG-ASN : angle 23.48123 ( 21) link_ALPHA1-6 : bond 0.00804 ( 7) link_ALPHA1-6 : angle 1.83313 ( 21) link_BETA1-4 : bond 0.00343 ( 12) link_BETA1-4 : angle 2.06847 ( 36) link_ALPHA1-2 : bond 0.00296 ( 6) link_ALPHA1-2 : angle 1.60908 ( 18) link_ALPHA1-3 : bond 0.00605 ( 6) link_ALPHA1-3 : angle 1.71625 ( 18) hydrogen bonds : bond 0.04080 ( 843) hydrogen bonds : angle 3.84118 ( 2697) SS BOND : bond 0.01875 ( 6) SS BOND : angle 2.59324 ( 12) covalent geometry : bond 0.00368 (17495) covalent geometry : angle 0.53267 (23859) *********************** 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 231 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 140 MET cc_start: 0.9005 (mmm) cc_final: 0.8756 (mmm) REVERT: C 300 PHE cc_start: 0.7964 (t80) cc_final: 0.7732 (t80) REVERT: C 314 ILE cc_start: 0.7996 (mm) cc_final: 0.7767 (mt) REVERT: C 349 MET cc_start: 0.4610 (tpt) cc_final: 0.4291 (tpt) REVERT: D 287 GLN cc_start: 0.8272 (mt0) cc_final: 0.8062 (mt0) REVERT: B 256 SER cc_start: 0.8673 (m) cc_final: 0.8298 (p) REVERT: B 339 MET cc_start: 0.3346 (tpp) cc_final: 0.3032 (mmt) outliers start: 21 outliers final: 15 residues processed: 221 average time/residue: 2.6418 time to fit residues: 690.3702 Evaluate side-chains 216 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 3.330 ------------------------------------------------------------------------------- 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 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 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 25 optimal weight: 0.8980 chunk 199 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 450 GLN C 62 ASN D 116 ASN D 331 ASN D 495 GLN B 176 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.137223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089790 restraints weight = 59083.417| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.21 r_work: 0.3069 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 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 = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 17539 Z= 0.182 Angle : 0.885 42.734 23985 Z= 0.359 Chirality : 0.047 0.479 2866 Planarity : 0.004 0.046 2913 Dihedral : 8.600 114.854 3001 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.28 % Allowed : 12.97 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 2024 helix: 3.04 (0.18), residues: 782 sheet: -0.06 (0.25), residues: 420 loop : -0.10 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 192 HIS 0.004 0.001 HIS B 498 PHE 0.016 0.001 PHE B 289 TYR 0.011 0.001 TYR B 127 ARG 0.006 0.000 ARG D 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 7) link_NAG-ASN : angle 23.37832 ( 21) link_ALPHA1-6 : bond 0.00786 ( 7) link_ALPHA1-6 : angle 1.90516 ( 21) link_BETA1-4 : bond 0.00368 ( 12) link_BETA1-4 : angle 2.10043 ( 36) link_ALPHA1-2 : bond 0.00283 ( 6) link_ALPHA1-2 : angle 1.62857 ( 18) link_ALPHA1-3 : bond 0.00582 ( 6) link_ALPHA1-3 : angle 1.67659 ( 18) hydrogen bonds : bond 0.04169 ( 843) hydrogen bonds : angle 3.84793 ( 2697) SS BOND : bond 0.02067 ( 6) SS BOND : angle 3.06106 ( 12) covalent geometry : bond 0.00423 (17495) covalent geometry : angle 0.53661 (23859) *********************** 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 226 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 140 MET cc_start: 0.9010 (mmm) cc_final: 0.8758 (mmm) REVERT: C 300 PHE cc_start: 0.7979 (t80) cc_final: 0.7740 (t80) REVERT: C 349 MET cc_start: 0.4830 (tpt) cc_final: 0.4473 (tpt) REVERT: D 287 GLN cc_start: 0.8283 (mt0) cc_final: 0.8080 (mt0) REVERT: B 256 SER cc_start: 0.8700 (m) cc_final: 0.8343 (p) REVERT: B 293 LYS cc_start: 0.8256 (mtpt) cc_final: 0.8042 (mtpp) REVERT: B 339 MET cc_start: 0.3322 (tpp) cc_final: 0.3008 (mmt) outliers start: 24 outliers final: 17 residues processed: 214 average time/residue: 2.0647 time to fit residues: 514.1010 Evaluate side-chains 216 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 2.598 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 126 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 450 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 = 0.3742 r_free = 0.3742 target = 0.137247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089958 restraints weight = 58959.816| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.21 r_work: 0.3068 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- 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 = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17539 Z= 0.158 Angle : 0.884 42.826 23985 Z= 0.358 Chirality : 0.046 0.478 2866 Planarity : 0.004 0.047 2913 Dihedral : 8.483 111.503 3001 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.17 % Allowed : 13.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 2024 helix: 3.06 (0.18), residues: 782 sheet: -0.11 (0.24), residues: 423 loop : -0.09 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 80 HIS 0.003 0.001 HIS C 45 PHE 0.013 0.001 PHE E 36 TYR 0.010 0.001 TYR B 127 ARG 0.007 0.000 ARG D 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 7) link_NAG-ASN : angle 23.49238 ( 21) link_ALPHA1-6 : bond 0.00752 ( 7) link_ALPHA1-6 : angle 1.94364 ( 21) link_BETA1-4 : bond 0.00341 ( 12) link_BETA1-4 : angle 2.02878 ( 36) link_ALPHA1-2 : bond 0.00289 ( 6) link_ALPHA1-2 : angle 1.61500 ( 18) link_ALPHA1-3 : bond 0.00595 ( 6) link_ALPHA1-3 : angle 1.63923 ( 18) hydrogen bonds : bond 0.04073 ( 843) hydrogen bonds : angle 3.83589 ( 2697) SS BOND : bond 0.02127 ( 6) SS BOND : angle 2.96711 ( 12) covalent geometry : bond 0.00362 (17495) covalent geometry : angle 0.53033 (23859) *********************** 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 222 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 314 ILE cc_start: 0.8012 (mm) cc_final: 0.7751 (mt) REVERT: C 349 MET cc_start: 0.4864 (tpt) cc_final: 0.4562 (tpt) REVERT: D 466 ARG cc_start: 0.6937 (mtp85) cc_final: 0.6663 (mtp180) REVERT: B 256 SER cc_start: 0.8695 (m) cc_final: 0.8347 (p) REVERT: B 293 LYS cc_start: 0.8263 (mtpt) cc_final: 0.8044 (mtpp) REVERT: B 339 MET cc_start: 0.3328 (tpp) cc_final: 0.3004 (mmt) outliers start: 22 outliers final: 18 residues processed: 211 average time/residue: 2.1147 time to fit residues: 517.5742 Evaluate side-chains 214 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 2.692 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 12 optimal weight: 0.5980 chunk 87 optimal weight: 0.0980 chunk 185 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 166 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 195 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 450 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 = 0.3747 r_free = 0.3747 target = 0.137615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.090398 restraints weight = 58941.603| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.21 r_work: 0.3073 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 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 = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 17539 Z= 0.143 Angle : 0.886 42.906 23985 Z= 0.357 Chirality : 0.046 0.490 2866 Planarity : 0.004 0.049 2913 Dihedral : 8.313 107.416 3001 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.23 % Allowed : 13.13 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.19), residues: 2024 helix: 3.11 (0.18), residues: 783 sheet: -0.09 (0.24), residues: 426 loop : -0.07 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 80 HIS 0.002 0.001 HIS B 498 PHE 0.017 0.001 PHE B 289 TYR 0.009 0.001 TYR B 139 ARG 0.008 0.000 ARG D 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 7) link_NAG-ASN : angle 23.58389 ( 21) link_ALPHA1-6 : bond 0.00759 ( 7) link_ALPHA1-6 : angle 1.94883 ( 21) link_BETA1-4 : bond 0.00330 ( 12) link_BETA1-4 : angle 1.97149 ( 36) link_ALPHA1-2 : bond 0.00288 ( 6) link_ALPHA1-2 : angle 1.60643 ( 18) link_ALPHA1-3 : bond 0.00597 ( 6) link_ALPHA1-3 : angle 1.62497 ( 18) hydrogen bonds : bond 0.03990 ( 843) hydrogen bonds : angle 3.79566 ( 2697) SS BOND : bond 0.02070 ( 6) SS BOND : angle 3.89017 ( 12) covalent geometry : bond 0.00329 (17495) covalent geometry : angle 0.52837 (23859) *********************** 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 222 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 314 ILE cc_start: 0.8028 (mm) cc_final: 0.7770 (mt) REVERT: C 349 MET cc_start: 0.4899 (tpt) cc_final: 0.4626 (tpt) REVERT: D 313 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7886 (mm) REVERT: D 466 ARG cc_start: 0.6938 (mtp85) cc_final: 0.6659 (mtp180) REVERT: B 256 SER cc_start: 0.8694 (m) cc_final: 0.8353 (p) REVERT: B 293 LYS cc_start: 0.8235 (mtpt) cc_final: 0.8017 (mtpp) REVERT: B 339 MET cc_start: 0.3222 (tpp) cc_final: 0.2906 (mmt) outliers start: 23 outliers final: 18 residues processed: 212 average time/residue: 2.2119 time to fit residues: 551.1951 Evaluate side-chains 216 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 2.519 ------------------------------------------------------------------------------- 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 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 313 LEU Chi-restraints excluded: chain D residue 490 GLN Chi-restraints excluded: chain B residue 46 HIS 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 22 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 190 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 47 optimal weight: 0.0020 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 450 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 = 0.3743 r_free = 0.3743 target = 0.137266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090158 restraints weight = 58910.851| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.21 r_work: 0.3070 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 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 = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 17539 Z= 0.157 Angle : 0.896 42.848 23985 Z= 0.363 Chirality : 0.046 0.499 2866 Planarity : 0.004 0.052 2913 Dihedral : 8.246 104.146 3001 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.17 % Allowed : 13.29 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.19), residues: 2024 helix: 3.11 (0.18), residues: 784 sheet: -0.08 (0.24), residues: 422 loop : -0.12 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 80 HIS 0.003 0.001 HIS B 498 PHE 0.016 0.001 PHE B 289 TYR 0.011 0.001 TYR B 139 ARG 0.007 0.000 ARG D 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 7) link_NAG-ASN : angle 23.51764 ( 21) link_ALPHA1-6 : bond 0.00725 ( 7) link_ALPHA1-6 : angle 1.96348 ( 21) link_BETA1-4 : bond 0.00345 ( 12) link_BETA1-4 : angle 1.98997 ( 36) link_ALPHA1-2 : bond 0.00274 ( 6) link_ALPHA1-2 : angle 1.62539 ( 18) link_ALPHA1-3 : bond 0.00582 ( 6) link_ALPHA1-3 : angle 1.61976 ( 18) hydrogen bonds : bond 0.04003 ( 843) hydrogen bonds : angle 3.79213 ( 2697) SS BOND : bond 0.01961 ( 6) SS BOND : angle 4.22388 ( 12) covalent geometry : bond 0.00366 (17495) covalent geometry : angle 0.54589 (23859) ********************** 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 224 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 4.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 314 ILE cc_start: 0.8040 (mm) cc_final: 0.7784 (mt) REVERT: C 349 MET cc_start: 0.5032 (tpt) cc_final: 0.4723 (tpt) REVERT: D 313 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7907 (mm) REVERT: D 466 ARG cc_start: 0.6962 (mtp85) cc_final: 0.6682 (mtp180) REVERT: B 256 SER cc_start: 0.8704 (m) cc_final: 0.8364 (p) REVERT: B 293 LYS cc_start: 0.8253 (mtpt) cc_final: 0.8051 (mtpp) REVERT: B 339 MET cc_start: 0.3259 (tpp) cc_final: 0.2937 (mmt) outliers start: 22 outliers final: 18 residues processed: 215 average time/residue: 2.2533 time to fit residues: 565.8257 Evaluate side-chains 221 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 2.431 ------------------------------------------------------------------------------- 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 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 313 LEU Chi-restraints excluded: chain D residue 490 GLN Chi-restraints excluded: chain B residue 46 HIS 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 18 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 63 optimal weight: 0.0070 chunk 117 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 53 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 450 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 = 0.3757 r_free = 0.3757 target = 0.138194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.091661 restraints weight = 58906.758| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.18 r_work: 0.3086 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 17539 Z= 0.133 Angle : 0.886 42.937 23985 Z= 0.356 Chirality : 0.045 0.493 2866 Planarity : 0.004 0.051 2913 Dihedral : 8.024 100.377 3001 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.01 % Allowed : 13.51 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 2024 helix: 3.18 (0.18), residues: 784 sheet: -0.10 (0.24), residues: 426 loop : -0.05 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 80 HIS 0.003 0.001 HIS E 199 PHE 0.017 0.001 PHE B 289 TYR 0.010 0.001 TYR B 139 ARG 0.008 0.000 ARG D 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 7) link_NAG-ASN : angle 23.67705 ( 21) link_ALPHA1-6 : bond 0.00758 ( 7) link_ALPHA1-6 : angle 1.95324 ( 21) link_BETA1-4 : bond 0.00316 ( 12) link_BETA1-4 : angle 1.91070 ( 36) link_ALPHA1-2 : bond 0.00301 ( 6) link_ALPHA1-2 : angle 1.58919 ( 18) link_ALPHA1-3 : bond 0.00610 ( 6) link_ALPHA1-3 : angle 1.60382 ( 18) hydrogen bonds : bond 0.03867 ( 843) hydrogen bonds : angle 3.73852 ( 2697) SS BOND : bond 0.01893 ( 6) SS BOND : angle 4.23926 ( 12) covalent geometry : bond 0.00306 (17495) covalent geometry : angle 0.52366 (23859) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30192.09 seconds wall clock time: 524 minutes 30.92 seconds (31470.92 seconds total)