Starting phenix.real_space_refine on Tue Sep 15 01:32:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yel_72854/09_2026/9yel_72854_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yel_72854/09_2026/9yel_72854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yel_72854/09_2026/9yel_72854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yel_72854/09_2026/9yel_72854.map" model { file = "/net/cci-nas-00/data/ceres_data/9yel_72854/09_2026/9yel_72854_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yel_72854/09_2026/9yel_72854_trim.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 S 76 5.16 5 C 10883 2.51 5 N 2689 2.21 5 O 3086 1.98 5 F 3 1.80 5 H 16488 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33225 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 6393 Classifications: {'peptide': 397} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 376} Chain breaks: 2 Chain: "C" Number of atoms: 6428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 6428 Classifications: {'peptide': 398} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 377} Chain breaks: 1 Chain: "E" Number of atoms: 6577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6577 Classifications: {'peptide': 405} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 379} Chain breaks: 3 Chain: "D" Number of atoms: 7025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 7025 Classifications: {'peptide': 431} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 400} Chain breaks: 1 Chain: "B" Number of atoms: 6483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6483 Classifications: {'peptide': 411} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 387} Chain breaks: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} 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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'RFX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 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} Time building chain proxies: 6.10, per 1000 atoms: 0.18 Number of scatterers: 33225 At special positions: 0 Unit cell: (100.98, 103.785, 169.235, 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 76 16.00 F 3 9.00 O 3086 8.00 N 2689 7.00 C 10883 6.00 H 16488 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.07 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.06 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.06 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 470 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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-ASN " NAG B 502 " - " ASN B 66 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN C 141 " " NAG H 1 " - " ASN E 141 " " NAG I 1 " - " ASN D 143 " " NAG J 1 " - " ASN B 141 " Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.3 seconds 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3906 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 19 sheets defined 45.1% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.526A pdb=" N PHE A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.118A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.946A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 262 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.768A pdb=" N ILE A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 437 removed outlier: 4.653A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.971A pdb=" N GLY C 73 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 218 through 229 Processing helix chain 'C' and resid 230 through 234 Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 241 through 263 Processing helix chain 'C' and resid 272 through 300 Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.611A pdb=" N ASP C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 removed outlier: 3.867A pdb=" N ILE C 323 " --> pdb=" O THR C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 436 removed outlier: 4.352A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 63 through 66 removed outlier: 3.624A pdb=" N SER E 66 " --> pdb=" O TYR E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.056A pdb=" N ASP E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 252 through 273 Processing helix chain 'E' and resid 283 through 311 Processing helix chain 'E' and resid 320 through 329 Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.813A pdb=" N TYR E 334 " --> pdb=" O LYS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 469 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.945A pdb=" N GLY D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.565A pdb=" N VAL D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 255 through 276 Processing helix chain 'D' and resid 286 through 314 Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.842A pdb=" N GLU D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 473 Proline residue: D 416 - end of helix Proline residue: D 458 - end of helix removed outlier: 3.627A pdb=" N GLN D 470 " --> pdb=" O TRP D 466 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.601A pdb=" N ARG B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 removed outlier: 3.526A pdb=" N ASN B 66 " --> pdb=" O TYR B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 66' Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.099A pdb=" N GLY B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 175 through 179 removed outlier: 4.001A pdb=" N TYR B 179 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 251 through 272 Processing helix chain 'B' and resid 282 through 310 Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.575A pdb=" N ARG B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 460 removed outlier: 3.618A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.169A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.169A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 49 " --> pdb=" O ASN A 42 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN A 42 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 40 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL A 61 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU A 30 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.287A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR A 196 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N TYR A 190 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 208 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.193A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.193A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE C 49 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN C 42 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASN C 53 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL C 61 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU C 30 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.167A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR C 196 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N THR C 189 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 198 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER C 187 " --> pdb=" O TYR C 198 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP C 200 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS C 185 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR C 202 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY C 183 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N HIS C 204 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER C 181 " --> pdb=" O HIS C 204 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL C 206 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.094A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.094A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU E 43 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU E 37 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP E 57 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU E 35 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLU E 59 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL E 33 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N THR E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL E 31 " --> pdb=" O THR E 61 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.790A pdb=" N ILE E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 82 removed outlier: 4.067A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 79 through 82 removed outlier: 4.067A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN D 55 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU D 42 " --> pdb=" O ASN D 55 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TRP D 57 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N SER D 40 " --> pdb=" O TRP D 57 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N GLU D 59 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR D 38 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLY D 61 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA D 36 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N THR D 63 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N ALA D 34 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N ASN D 65 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 14.007A pdb=" N ASP D 32 " --> pdb=" O ASN D 65 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 94 removed outlier: 5.281A pdb=" N SER D 150 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN D 213 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE D 220 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 92 through 94 removed outlier: 5.281A pdb=" N SER D 150 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN D 213 " --> pdb=" O SER D 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AB7, first strand: chain 'B' and resid 79 through 81 Processing sheet with id=AB8, first strand: chain 'B' and resid 79 through 81 removed outlier: 6.956A pdb=" N THR B 49 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER B 42 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR B 51 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 40 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER B 53 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN B 61 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR B 30 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.041A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE B 215 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.041A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) 965 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.21 Time building geometry restraints manager: 5.17 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: 16469 1.04 - 1.23: 340 1.23 - 1.43: 6832 1.43 - 1.62: 9885 1.62 - 1.82: 121 Bond restraints: 33647 Sorted by residual: bond pdb=" C CYS B 142 " pdb=" O CYS B 142 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.21e-02 6.83e+03 1.97e+01 bond pdb=" CA SER C 248 " pdb=" CB SER C 248 " ideal model delta sigma weight residual 1.530 1.459 0.071 1.68e-02 3.54e+03 1.77e+01 bond pdb=" NZ LYS D 276 " pdb=" HZ3 LYS D 276 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS B 167 " pdb=" HZ2 LYS B 167 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS C 107 " pdb=" HZ3 LYS C 107 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 33642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.84: 60866 12.84 - 25.68: 2 25.68 - 38.52: 1 38.52 - 51.36: 2 51.36 - 64.20: 3 Bond angle restraints: 60874 Sorted by residual: angle pdb=" CA ALA B 397 " pdb=" N ALA B 397 " pdb=" H ALA B 397 " ideal model delta sigma weight residual 114.00 178.20 -64.20 3.00e+00 1.11e-01 4.58e+02 angle pdb=" CA LEU E 407 " pdb=" N LEU E 407 " pdb=" H LEU E 407 " ideal model delta sigma weight residual 114.00 177.03 -63.03 3.00e+00 1.11e-01 4.41e+02 angle pdb=" CA LEU D 410 " pdb=" N LEU D 410 " pdb=" H LEU D 410 " ideal model delta sigma weight residual 114.00 172.82 -58.82 3.00e+00 1.11e-01 3.84e+02 angle pdb=" CA HIS A 369 " pdb=" N HIS A 369 " pdb=" H HIS A 369 " ideal model delta sigma weight residual 114.00 157.98 -43.98 3.00e+00 1.11e-01 2.15e+02 angle pdb=" CA HIS C 369 " pdb=" N HIS C 369 " pdb=" H HIS C 369 " ideal model delta sigma weight residual 114.00 156.23 -42.23 3.00e+00 1.11e-01 1.98e+02 ... (remaining 60869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 15042 21.13 - 42.26: 800 42.26 - 63.40: 260 63.40 - 84.53: 61 84.53 - 105.66: 27 Dihedral angle restraints: 16190 sinusoidal: 8937 harmonic: 7253 Sorted by residual: dihedral pdb=" O4 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C5 BMA J 3 " pdb=" O5 BMA J 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.95 105.66 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.77 105.48 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.59 105.30 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 16187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2525 0.083 - 0.165: 245 0.165 - 0.248: 6 0.248 - 0.331: 2 0.331 - 0.413: 1 Chirality restraints: 2779 Sorted by residual: 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 -2.56 0.16 2.00e-02 2.50e+03 6.29e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.28e+01 chirality pdb=" C1 MAN F 5 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 5 " pdb=" O5 MAN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.31 0.09 2.00e-02 2.50e+03 2.00e+01 ... (remaining 2776 not shown) Planarity restraints: 4812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " 0.181 2.00e-02 2.50e+03 1.50e-01 2.83e+02 pdb=" C7 NAG B 502 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " 0.130 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " -0.247 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.077 2.00e-02 2.50e+03 6.52e-02 5.32e+01 pdb=" C7 NAG G 2 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.019 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.106 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.066 2.00e-02 2.50e+03 5.56e-02 3.87e+01 pdb=" C7 NAG H 2 " 0.017 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.017 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.087 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.055 2.00e-02 2.50e+03 ... (remaining 4809 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.00: 191 2.00 - 2.65: 44463 2.65 - 3.30: 99181 3.30 - 3.95: 132256 3.95 - 4.60: 204260 Nonbonded interactions: 480351 Sorted by model distance: nonbonded pdb=" HH TYR B 15 " pdb=" H TRP B 86 " model vdw 1.356 2.100 nonbonded pdb=" HG1 THR C 229 " pdb="HG22 VAL C 285 " model vdw 1.502 2.270 nonbonded pdb=" HH TYR E 15 " pdb=" H TRP E 86 " model vdw 1.522 2.100 nonbonded pdb=" HG1 THR C 150 " pdb="HD21 ASN D 109 " model vdw 1.605 2.100 nonbonded pdb=" HG SER D 105 " pdb=" H ILE D 125 " model vdw 1.634 2.100 ... (remaining 480346 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 1 through 436 or resid 501)) selection = (chain 'C' and (resid 1 through 325 or resid 327 through 329 or resid 369 throug \ h 501)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.250 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 33.880 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.004 0.071 17187 Z= 0.212 Angle : 0.682 7.106 23487 Z= 0.348 Chirality : 0.048 0.413 2779 Planarity : 0.006 0.150 2895 Dihedral : 16.678 105.659 6548 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.64 % Favored : 98.31 % Rotamer: Outliers : 0.21 % Allowed : 8.74 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 2016 helix: 2.38 (0.17), residues: 787 sheet: -0.70 (0.25), residues: 361 loop : -0.13 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 446 TYR 0.008 0.001 TYR B 67 PHE 0.012 0.001 PHE A 284 TRP 0.007 0.001 TRP C 311 HIS 0.004 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.21 (17159) covalent geometry : angle 0.66438 / 0.34 (23409) SS BOND : bond 0.02487 / 1.23 ( 6) SS BOND : angle 3.40600 / 1.91 ( 12) hydrogen bonds : bond 0.14413 / 9.61 ( 882) hydrogen bonds : angle 6.06068 / 4.36 ( 2796) link_ALPHA1-3 : bond 0.00246 / 0.12 ( 3) link_ALPHA1-3 : angle 1.79104 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00266 / 0.13 ( 3) link_ALPHA1-6 : angle 0.95960 / 0.51 ( 9) link_BETA1-4 : bond 0.00991 / 0.63 ( 10) link_BETA1-4 : angle 3.01689 / 1.88 ( 30) link_NAG-ASN : bond 0.02463 / 1.20 ( 6) link_NAG-ASN : angle 2.95806 / 1.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 309 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 MET cc_start: 0.6557 (ptm) cc_final: 0.6274 (mmt) REVERT: C 380 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7410 (mmmt) REVERT: C 387 LYS cc_start: 0.8162 (tptm) cc_final: 0.7852 (tptm) REVERT: C 394 ASN cc_start: 0.7626 (m-40) cc_final: 0.7224 (t0) REVERT: E 258 ILE cc_start: 0.8847 (mm) cc_final: 0.8627 (mt) REVERT: E 422 ARG cc_start: 0.7711 (ttp-170) cc_final: 0.7502 (ttp80) REVERT: E 461 LEU cc_start: 0.8379 (tp) cc_final: 0.8082 (mp) REVERT: E 466 ASP cc_start: 0.7847 (t0) cc_final: 0.7571 (t0) REVERT: E 471 LEU cc_start: 0.8300 (mt) cc_final: 0.8074 (mm) REVERT: D 2 ASN cc_start: 0.5953 (m-40) cc_final: 0.5740 (m-40) REVERT: D 431 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7901 (tt0) REVERT: D 460 MET cc_start: 0.7280 (ttt) cc_final: 0.7064 (ttm) REVERT: D 469 LEU cc_start: 0.8631 (mt) cc_final: 0.8355 (mp) REVERT: B 272 GLN cc_start: 0.7614 (pt0) cc_final: 0.7321 (mp10) REVERT: B 286 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7391 (mtp-110) REVERT: B 318 MET cc_start: 0.8250 (tpp) cc_final: 0.7468 (tpt) REVERT: B 408 ASN cc_start: 0.8518 (m-40) cc_final: 0.7722 (m110) REVERT: B 429 ARG cc_start: 0.7292 (mtm-85) cc_final: 0.7054 (mtm180) outliers start: 4 outliers final: 3 residues processed: 313 average time/residue: 1.1589 time to fit residues: 413.9048 Evaluate side-chains 222 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 219 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain D residue 326 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 169 ASN D 200 ASN D 267 GLN B 99 GLN B 247 GLN B 263 GLN B 310 GLN B 316 HIS B 432 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114143 restraints weight = 56738.345| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.81 r_work: 0.3277 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17187 Z= 0.166 Angle : 0.554 5.159 23487 Z= 0.280 Chirality : 0.045 0.199 2779 Planarity : 0.004 0.049 2895 Dihedral : 10.834 89.224 2651 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.59 % Favored : 98.36 % Rotamer: Outliers : 1.34 % Allowed : 12.18 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.19), residues: 2016 helix: 2.71 (0.17), residues: 789 sheet: -0.53 (0.25), residues: 381 loop : -0.09 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 9 TYR 0.014 0.001 TYR D 434 PHE 0.011 0.001 PHE A 12 TRP 0.009 0.001 TRP D 62 HIS 0.005 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (17159) covalent geometry : angle 0.54025 / 0.28 (23409) SS BOND : bond 0.00431 / 0.21 ( 6) SS BOND : angle 1.54293 / 0.89 ( 12) hydrogen bonds : bond 0.04609 / 3.11 ( 882) hydrogen bonds : angle 4.47192 / 3.20 ( 2796) link_ALPHA1-3 : bond 0.00669 / 0.33 ( 3) link_ALPHA1-3 : angle 2.29689 / 1.23 ( 9) link_ALPHA1-6 : bond 0.00478 / 0.24 ( 3) link_ALPHA1-6 : angle 2.07424 / 1.15 ( 9) link_BETA1-4 : bond 0.00371 / 0.21 ( 10) link_BETA1-4 : angle 2.50642 / 1.77 ( 30) link_NAG-ASN : bond 0.00373 / 0.18 ( 6) link_NAG-ASN : angle 2.17700 / 1.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 THR cc_start: 0.3535 (OUTLIER) cc_final: 0.3264 (t) REVERT: A 329 MET cc_start: 0.4049 (mpp) cc_final: 0.3038 (mmm) REVERT: A 384 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7742 (mm-30) REVERT: A 387 LYS cc_start: 0.8476 (mmmm) cc_final: 0.7430 (mttt) REVERT: A 415 MET cc_start: 0.6676 (ptm) cc_final: 0.6106 (tpp) REVERT: C 324 MET cc_start: 0.5750 (mtp) cc_final: 0.5143 (mtp) REVERT: C 380 LYS cc_start: 0.7642 (mtpt) cc_final: 0.7136 (mmmt) REVERT: C 410 LEU cc_start: 0.7284 (mm) cc_final: 0.7054 (mt) REVERT: E 461 LEU cc_start: 0.7937 (tp) cc_final: 0.7555 (mt) REVERT: E 466 ASP cc_start: 0.7858 (t0) cc_final: 0.7510 (t0) REVERT: D 2 ASN cc_start: 0.6332 (m-40) cc_final: 0.5999 (m-40) REVERT: D 301 MET cc_start: 0.8352 (mtp) cc_final: 0.8042 (mtt) REVERT: D 431 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7650 (tt0) REVERT: D 449 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7486 (t0) REVERT: B 131 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: B 149 GLN cc_start: 0.7798 (tt0) cc_final: 0.7533 (pt0) REVERT: B 225 ILE cc_start: 0.8476 (mt) cc_final: 0.8226 (mm) REVERT: B 272 GLN cc_start: 0.7627 (pt0) cc_final: 0.7048 (mt0) REVERT: B 286 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7116 (mtp180) REVERT: B 408 ASN cc_start: 0.8350 (m-40) cc_final: 0.7633 (m110) REVERT: B 429 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.7232 (mtm180) outliers start: 25 outliers final: 7 residues processed: 244 average time/residue: 1.1297 time to fit residues: 314.5552 Evaluate side-chains 226 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 216 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 197 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 HIS C 394 ASN D 267 GLN D 442 ASN B 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.140260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113211 restraints weight = 56291.766| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.77 r_work: 0.3263 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17187 Z= 0.173 Angle : 0.539 5.723 23487 Z= 0.270 Chirality : 0.044 0.223 2779 Planarity : 0.004 0.040 2895 Dihedral : 9.547 86.411 2648 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.84 % Favored : 98.12 % Rotamer: Outliers : 1.39 % Allowed : 12.61 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 2016 helix: 2.72 (0.17), residues: 790 sheet: -0.47 (0.26), residues: 381 loop : -0.18 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 81 TYR 0.012 0.001 TYR D 434 PHE 0.011 0.001 PHE B 439 TRP 0.008 0.001 TRP D 62 HIS 0.005 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (17159) covalent geometry : angle 0.52610 / 0.27 (23409) SS BOND : bond 0.00441 / 0.22 ( 6) SS BOND : angle 1.54465 / 0.89 ( 12) hydrogen bonds : bond 0.04407 / 2.95 ( 882) hydrogen bonds : angle 4.27945 / 3.06 ( 2796) link_ALPHA1-3 : bond 0.00797 / 0.39 ( 3) link_ALPHA1-3 : angle 1.76843 / 0.97 ( 9) link_ALPHA1-6 : bond 0.00649 / 0.32 ( 3) link_ALPHA1-6 : angle 2.04446 / 1.11 ( 9) link_BETA1-4 : bond 0.00476 / 0.29 ( 10) link_BETA1-4 : angle 2.49099 / 1.75 ( 30) link_NAG-ASN : bond 0.00390 / 0.19 ( 6) link_NAG-ASN : angle 1.89143 / 1.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7790 (mm-30) REVERT: A 387 LYS cc_start: 0.8490 (mmmm) cc_final: 0.7403 (mttt) REVERT: A 415 MET cc_start: 0.6738 (ptm) cc_final: 0.6126 (tpp) REVERT: C 324 MET cc_start: 0.5533 (mtp) cc_final: 0.5208 (mtp) REVERT: C 380 LYS cc_start: 0.7670 (mtpt) cc_final: 0.7171 (mmmt) REVERT: E 44 ASN cc_start: 0.8711 (t0) cc_final: 0.8412 (t0) REVERT: E 273 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7092 (m-30) REVERT: E 461 LEU cc_start: 0.7945 (tp) cc_final: 0.7536 (mp) REVERT: E 466 ASP cc_start: 0.7831 (t0) cc_final: 0.7494 (t0) REVERT: D 2 ASN cc_start: 0.6478 (m-40) cc_final: 0.6138 (m-40) REVERT: D 431 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7642 (tt0) REVERT: B 131 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: B 149 GLN cc_start: 0.7825 (tt0) cc_final: 0.7545 (pt0) REVERT: B 225 ILE cc_start: 0.8563 (mt) cc_final: 0.8306 (mm) REVERT: B 272 GLN cc_start: 0.7704 (pt0) cc_final: 0.7096 (mt0) REVERT: B 286 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7199 (mtp-110) REVERT: B 408 ASN cc_start: 0.8353 (m-40) cc_final: 0.7622 (m110) REVERT: B 429 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.7241 (mtm180) outliers start: 26 outliers final: 8 residues processed: 241 average time/residue: 1.1161 time to fit residues: 307.6778 Evaluate side-chains 227 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 217 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 131 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 129 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN C 394 ASN D 267 GLN D 442 ASN B 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112560 restraints weight = 56286.707| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.76 r_work: 0.3256 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17187 Z= 0.187 Angle : 0.541 6.411 23487 Z= 0.272 Chirality : 0.044 0.231 2779 Planarity : 0.004 0.040 2895 Dihedral : 9.117 87.579 2648 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.84 % Favored : 98.12 % Rotamer: Outliers : 1.56 % Allowed : 12.66 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.19), residues: 2016 helix: 2.71 (0.17), residues: 791 sheet: -0.47 (0.26), residues: 382 loop : -0.25 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.013 0.001 TYR D 434 PHE 0.012 0.001 PHE E 12 TRP 0.008 0.001 TRP D 62 HIS 0.004 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (17159) covalent geometry : angle 0.52790 / 0.27 (23409) SS BOND : bond 0.00437 / 0.22 ( 6) SS BOND : angle 1.54316 / 0.89 ( 12) hydrogen bonds : bond 0.04276 / 2.86 ( 882) hydrogen bonds : angle 4.21835 / 3.01 ( 2796) link_ALPHA1-3 : bond 0.00789 / 0.38 ( 3) link_ALPHA1-3 : angle 1.93272 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00629 / 0.31 ( 3) link_ALPHA1-6 : angle 2.10700 / 1.14 ( 9) link_BETA1-4 : bond 0.00415 / 0.26 ( 10) link_BETA1-4 : angle 2.40108 / 1.64 ( 30) link_NAG-ASN : bond 0.00357 / 0.17 ( 6) link_NAG-ASN : angle 1.88174 / 1.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LYS cc_start: 0.8487 (mmmm) cc_final: 0.7400 (mttt) REVERT: A 415 MET cc_start: 0.6646 (ptm) cc_final: 0.5994 (mmt) REVERT: C 324 MET cc_start: 0.5477 (mtp) cc_final: 0.5009 (mtp) REVERT: C 380 LYS cc_start: 0.7611 (mtpt) cc_final: 0.7124 (mmmt) REVERT: E 44 ASN cc_start: 0.8716 (t0) cc_final: 0.8401 (t0) REVERT: E 273 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6983 (m-30) REVERT: E 461 LEU cc_start: 0.7936 (tp) cc_final: 0.7515 (mp) REVERT: E 466 ASP cc_start: 0.7846 (t0) cc_final: 0.7539 (t0) REVERT: D 272 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8098 (tp) REVERT: D 431 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7662 (tt0) REVERT: B 131 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: B 149 GLN cc_start: 0.7832 (tt0) cc_final: 0.7509 (pt0) REVERT: B 225 ILE cc_start: 0.8582 (mt) cc_final: 0.8317 (mm) REVERT: B 272 GLN cc_start: 0.7698 (pt0) cc_final: 0.7133 (mt0) REVERT: B 286 ARG cc_start: 0.7769 (mtt180) cc_final: 0.7173 (mtp180) REVERT: B 408 ASN cc_start: 0.8360 (m-40) cc_final: 0.7630 (m110) outliers start: 29 outliers final: 8 residues processed: 238 average time/residue: 1.1005 time to fit residues: 300.8939 Evaluate side-chains 227 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 131 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 104 optimal weight: 0.0870 chunk 153 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN C 394 ASN D 267 GLN D 442 ASN B 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.139715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112678 restraints weight = 56298.962| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.77 r_work: 0.3257 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17187 Z= 0.166 Angle : 0.524 5.319 23487 Z= 0.264 Chirality : 0.043 0.222 2779 Planarity : 0.004 0.040 2895 Dihedral : 8.725 89.879 2647 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.84 % Favored : 98.12 % Rotamer: Outliers : 1.29 % Allowed : 12.98 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 2016 helix: 2.76 (0.17), residues: 791 sheet: -0.49 (0.26), residues: 391 loop : -0.24 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 429 TYR 0.012 0.001 TYR D 434 PHE 0.012 0.001 PHE B 439 TRP 0.008 0.001 TRP C 311 HIS 0.004 0.001 HIS E 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (17159) covalent geometry : angle 0.51240 / 0.26 (23409) SS BOND : bond 0.00382 / 0.19 ( 6) SS BOND : angle 1.37725 / 0.80 ( 12) hydrogen bonds : bond 0.04173 / 2.78 ( 882) hydrogen bonds : angle 4.15430 / 2.97 ( 2796) link_ALPHA1-3 : bond 0.00813 / 0.40 ( 3) link_ALPHA1-3 : angle 1.91331 / 1.03 ( 9) link_ALPHA1-6 : bond 0.00657 / 0.32 ( 3) link_ALPHA1-6 : angle 1.97857 / 1.11 ( 9) link_BETA1-4 : bond 0.00404 / 0.25 ( 10) link_BETA1-4 : angle 2.21601 / 1.48 ( 30) link_NAG-ASN : bond 0.00282 / 0.14 ( 6) link_NAG-ASN : angle 1.79026 / 1.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LYS cc_start: 0.8491 (mmmm) cc_final: 0.7417 (mttt) REVERT: A 415 MET cc_start: 0.6614 (ptm) cc_final: 0.5936 (mmt) REVERT: C 324 MET cc_start: 0.5356 (mtp) cc_final: 0.5099 (mtp) REVERT: C 380 LYS cc_start: 0.7588 (mtpt) cc_final: 0.7127 (mmmt) REVERT: E 44 ASN cc_start: 0.8712 (t0) cc_final: 0.8386 (t0) REVERT: E 238 LEU cc_start: 0.8230 (tp) cc_final: 0.7868 (mm) REVERT: E 319 MET cc_start: 0.7561 (ttm) cc_final: 0.7355 (ttm) REVERT: E 427 GLN cc_start: 0.7706 (tt0) cc_final: 0.7225 (tm-30) REVERT: E 461 LEU cc_start: 0.7895 (tp) cc_final: 0.7479 (mp) REVERT: D 272 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8079 (tp) REVERT: D 431 GLN cc_start: 0.8204 (tp-100) cc_final: 0.7653 (tt0) REVERT: B 131 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: B 225 ILE cc_start: 0.8573 (mt) cc_final: 0.8310 (mm) REVERT: B 272 GLN cc_start: 0.7696 (pt0) cc_final: 0.7139 (mt0) REVERT: B 286 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7153 (mtp180) REVERT: B 408 ASN cc_start: 0.8415 (m-40) cc_final: 0.7711 (m110) REVERT: B 429 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7177 (mtm180) outliers start: 24 outliers final: 10 residues processed: 235 average time/residue: 1.0929 time to fit residues: 294.7154 Evaluate side-chains 225 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 464 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 99 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 201 optimal weight: 0.0270 chunk 140 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN A 186 HIS C 394 ASN D 267 GLN D 442 ASN B 432 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.140164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113129 restraints weight = 56345.316| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.77 r_work: 0.3264 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17187 Z= 0.143 Angle : 0.508 6.043 23487 Z= 0.255 Chirality : 0.043 0.182 2779 Planarity : 0.004 0.039 2895 Dihedral : 8.182 89.968 2647 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.08 % Favored : 97.87 % Rotamer: Outliers : 1.23 % Allowed : 13.52 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 2016 helix: 2.86 (0.17), residues: 791 sheet: -0.52 (0.25), residues: 391 loop : -0.22 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.011 0.001 TYR D 434 PHE 0.011 0.001 PHE B 439 TRP 0.008 0.001 TRP C 311 HIS 0.004 0.001 HIS E 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (17159) covalent geometry : angle 0.49761 / 0.25 (23409) SS BOND : bond 0.00325 / 0.17 ( 6) SS BOND : angle 1.21419 / 0.70 ( 12) hydrogen bonds : bond 0.04046 / 2.69 ( 882) hydrogen bonds : angle 4.07855 / 2.91 ( 2796) link_ALPHA1-3 : bond 0.00794 / 0.39 ( 3) link_ALPHA1-3 : angle 1.90311 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00848 / 0.42 ( 3) link_ALPHA1-6 : angle 1.86336 / 1.08 ( 9) link_BETA1-4 : bond 0.00358 / 0.22 ( 10) link_BETA1-4 : angle 2.08689 / 1.38 ( 30) link_NAG-ASN : bond 0.00210 / 0.10 ( 6) link_NAG-ASN : angle 1.72251 / 0.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.4382 (mpp) cc_final: 0.3723 (mmm) REVERT: A 387 LYS cc_start: 0.8527 (mmmm) cc_final: 0.7444 (mttt) REVERT: A 415 MET cc_start: 0.6588 (ptm) cc_final: 0.5869 (tpp) REVERT: C 324 MET cc_start: 0.5235 (mtp) cc_final: 0.4987 (mtp) REVERT: C 380 LYS cc_start: 0.7578 (mtpt) cc_final: 0.7118 (mmmt) REVERT: C 394 ASN cc_start: 0.7407 (m-40) cc_final: 0.6864 (t0) REVERT: E 44 ASN cc_start: 0.8715 (t0) cc_final: 0.8382 (t0) REVERT: E 238 LEU cc_start: 0.8228 (tp) cc_final: 0.7867 (mm) REVERT: E 461 LEU cc_start: 0.7899 (tp) cc_final: 0.7486 (mp) REVERT: D 272 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8036 (tp) REVERT: D 431 GLN cc_start: 0.8178 (tp-100) cc_final: 0.7796 (mt0) REVERT: B 131 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: B 225 ILE cc_start: 0.8564 (mt) cc_final: 0.8301 (mm) REVERT: B 272 GLN cc_start: 0.7712 (pt0) cc_final: 0.7128 (mt0) REVERT: B 286 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7031 (mtp180) REVERT: B 408 ASN cc_start: 0.8398 (m-40) cc_final: 0.7700 (m110) REVERT: B 429 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7133 (mtm180) outliers start: 23 outliers final: 11 residues processed: 235 average time/residue: 1.0777 time to fit residues: 291.4521 Evaluate side-chains 226 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 464 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 123 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 136 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN D 267 GLN D 442 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113095 restraints weight = 56422.247| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.78 r_work: 0.3264 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17187 Z= 0.148 Angle : 0.507 5.137 23487 Z= 0.256 Chirality : 0.043 0.184 2779 Planarity : 0.004 0.039 2895 Dihedral : 7.859 88.983 2647 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.88 % Favored : 98.07 % Rotamer: Outliers : 0.86 % Allowed : 13.95 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 2016 helix: 2.87 (0.17), residues: 791 sheet: -0.51 (0.25), residues: 391 loop : -0.22 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.011 0.001 TYR D 434 PHE 0.010 0.001 PHE B 439 TRP 0.009 0.001 TRP C 311 HIS 0.005 0.001 HIS E 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (17159) covalent geometry : angle 0.49571 / 0.25 (23409) SS BOND : bond 0.00332 / 0.17 ( 6) SS BOND : angle 1.25024 / 0.72 ( 12) hydrogen bonds : bond 0.04033 / 2.68 ( 882) hydrogen bonds : angle 4.06198 / 2.90 ( 2796) link_ALPHA1-3 : bond 0.00841 / 0.41 ( 3) link_ALPHA1-3 : angle 1.73315 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00972 / 0.48 ( 3) link_ALPHA1-6 : angle 2.46258 / 1.32 ( 9) link_BETA1-4 : bond 0.00360 / 0.22 ( 10) link_BETA1-4 : angle 2.04571 / 1.34 ( 30) link_NAG-ASN : bond 0.00235 / 0.11 ( 6) link_NAG-ASN : angle 1.73121 / 1.00 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LYS cc_start: 0.8525 (mmmm) cc_final: 0.7447 (mttt) REVERT: A 415 MET cc_start: 0.6575 (ptm) cc_final: 0.5888 (mmt) REVERT: C 324 MET cc_start: 0.5071 (mtp) cc_final: 0.4839 (mtp) REVERT: C 380 LYS cc_start: 0.7588 (mtpt) cc_final: 0.7177 (mmmt) REVERT: E 44 ASN cc_start: 0.8720 (t0) cc_final: 0.8385 (t0) REVERT: E 59 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: E 427 GLN cc_start: 0.7709 (tt0) cc_final: 0.7220 (tm-30) REVERT: E 461 LEU cc_start: 0.7902 (tp) cc_final: 0.7488 (mp) REVERT: E 466 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7517 (t0) REVERT: D 431 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7853 (mt0) REVERT: B 131 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: B 225 ILE cc_start: 0.8562 (mt) cc_final: 0.8302 (mm) REVERT: B 272 GLN cc_start: 0.7687 (pt0) cc_final: 0.7108 (mt0) REVERT: B 286 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7029 (mtp180) REVERT: B 408 ASN cc_start: 0.8443 (m-40) cc_final: 0.7746 (m110) REVERT: B 429 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7133 (mtm180) outliers start: 16 outliers final: 8 residues processed: 227 average time/residue: 1.0990 time to fit residues: 286.5909 Evaluate side-chains 223 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 131 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 197 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 183 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN C 394 ASN D 267 GLN D 442 ASN B 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.138880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111809 restraints weight = 56147.005| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.76 r_work: 0.3246 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17187 Z= 0.195 Angle : 0.539 6.593 23487 Z= 0.272 Chirality : 0.044 0.176 2779 Planarity : 0.004 0.041 2895 Dihedral : 8.080 88.854 2647 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.08 % Favored : 97.87 % Rotamer: Outliers : 1.02 % Allowed : 13.89 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.19), residues: 2016 helix: 2.73 (0.17), residues: 792 sheet: -0.52 (0.25), residues: 391 loop : -0.29 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.012 0.001 TYR D 434 PHE 0.012 0.001 PHE B 439 TRP 0.008 0.001 TRP C 311 HIS 0.004 0.001 HIS E 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (17159) covalent geometry : angle 0.52774 / 0.27 (23409) SS BOND : bond 0.00424 / 0.22 ( 6) SS BOND : angle 1.55798 / 0.90 ( 12) hydrogen bonds : bond 0.04229 / 2.82 ( 882) hydrogen bonds : angle 4.15260 / 2.96 ( 2796) link_ALPHA1-3 : bond 0.00745 / 0.36 ( 3) link_ALPHA1-3 : angle 1.75270 / 0.96 ( 9) link_ALPHA1-6 : bond 0.00739 / 0.36 ( 3) link_ALPHA1-6 : angle 1.98229 / 1.12 ( 9) link_BETA1-4 : bond 0.00423 / 0.26 ( 10) link_BETA1-4 : angle 2.24372 / 1.45 ( 30) link_NAG-ASN : bond 0.00412 / 0.20 ( 6) link_NAG-ASN : angle 1.84136 / 1.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LYS cc_start: 0.8539 (mmmm) cc_final: 0.7442 (mttt) REVERT: A 415 MET cc_start: 0.6595 (ptm) cc_final: 0.5866 (mmt) REVERT: C 10 LYS cc_start: 0.8604 (tptp) cc_final: 0.8237 (tmmt) REVERT: C 324 MET cc_start: 0.5078 (mtp) cc_final: 0.4845 (mtp) REVERT: C 380 LYS cc_start: 0.7584 (mtpt) cc_final: 0.7119 (mmmt) REVERT: E 44 ASN cc_start: 0.8736 (t0) cc_final: 0.8423 (t0) REVERT: E 71 GLU cc_start: 0.7150 (mp0) cc_final: 0.6902 (mp0) REVERT: E 427 GLN cc_start: 0.7718 (tt0) cc_final: 0.7227 (tm-30) REVERT: E 461 LEU cc_start: 0.7932 (tp) cc_final: 0.7501 (mp) REVERT: D 431 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7790 (mt0) REVERT: B 14 ASN cc_start: 0.8465 (t0) cc_final: 0.8236 (m-40) REVERT: B 131 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: B 225 ILE cc_start: 0.8575 (mt) cc_final: 0.8315 (mm) REVERT: B 272 GLN cc_start: 0.7694 (pt0) cc_final: 0.7167 (mt0) REVERT: B 286 ARG cc_start: 0.7741 (mtt180) cc_final: 0.7146 (mtp180) REVERT: B 408 ASN cc_start: 0.8443 (m-40) cc_final: 0.7742 (m110) REVERT: B 429 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7129 (mtm180) outliers start: 19 outliers final: 10 residues processed: 231 average time/residue: 1.1049 time to fit residues: 292.3487 Evaluate side-chains 229 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 218 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 131 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 126 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 72 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 191 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN C 394 ASN D 267 GLN D 442 ASN D 475 GLN B 310 GLN B 432 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113923 restraints weight = 56008.763| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.78 r_work: 0.3275 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17187 Z= 0.112 Angle : 0.491 5.224 23487 Z= 0.248 Chirality : 0.042 0.190 2779 Planarity : 0.004 0.040 2895 Dihedral : 7.640 88.862 2647 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.97 % Rotamer: Outliers : 1.02 % Allowed : 14.11 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 2016 helix: 2.93 (0.17), residues: 791 sheet: -0.55 (0.25), residues: 390 loop : -0.20 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 429 TYR 0.012 0.001 TYR C 213 PHE 0.011 0.001 PHE B 439 TRP 0.009 0.001 TRP C 311 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (17159) covalent geometry : angle 0.48217 / 0.25 (23409) SS BOND : bond 0.00228 / 0.11 ( 6) SS BOND : angle 0.90879 / 0.52 ( 12) hydrogen bonds : bond 0.03902 / 2.59 ( 882) hydrogen bonds : angle 4.01345 / 2.87 ( 2796) link_ALPHA1-3 : bond 0.00776 / 0.38 ( 3) link_ALPHA1-3 : angle 1.76392 / 0.93 ( 9) link_ALPHA1-6 : bond 0.00812 / 0.40 ( 3) link_ALPHA1-6 : angle 2.05111 / 1.16 ( 9) link_BETA1-4 : bond 0.00312 / 0.20 ( 10) link_BETA1-4 : angle 1.82130 / 1.22 ( 30) link_NAG-ASN : bond 0.00125 / 0.08 ( 6) link_NAG-ASN : angle 1.58111 / 0.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7720 (mm-30) REVERT: A 387 LYS cc_start: 0.8524 (mmmm) cc_final: 0.7435 (mttt) REVERT: A 415 MET cc_start: 0.6590 (ptm) cc_final: 0.5863 (mmt) REVERT: C 259 VAL cc_start: 0.8145 (t) cc_final: 0.7939 (m) REVERT: C 380 LYS cc_start: 0.7584 (mtpt) cc_final: 0.7171 (mmmt) REVERT: C 394 ASN cc_start: 0.7310 (m-40) cc_final: 0.6817 (t0) REVERT: E 44 ASN cc_start: 0.8697 (t0) cc_final: 0.8363 (t0) REVERT: E 71 GLU cc_start: 0.7193 (mp0) cc_final: 0.6932 (mp0) REVERT: E 238 LEU cc_start: 0.8223 (tp) cc_final: 0.7878 (mm) REVERT: E 319 MET cc_start: 0.7435 (ttm) cc_final: 0.7232 (ttm) REVERT: E 427 GLN cc_start: 0.7706 (tt0) cc_final: 0.7234 (tm-30) REVERT: E 461 LEU cc_start: 0.7927 (tp) cc_final: 0.7508 (mp) REVERT: E 466 ASP cc_start: 0.7966 (t70) cc_final: 0.7733 (t0) REVERT: D 186 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: D 272 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8067 (tp) REVERT: D 431 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7855 (mt0) REVERT: B 225 ILE cc_start: 0.8538 (mt) cc_final: 0.8281 (mm) REVERT: B 272 GLN cc_start: 0.7698 (pt0) cc_final: 0.7112 (mt0) REVERT: B 286 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7010 (mtp180) REVERT: B 408 ASN cc_start: 0.8456 (m-40) cc_final: 0.7743 (m110) REVERT: B 429 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7114 (mtm180) outliers start: 19 outliers final: 10 residues processed: 231 average time/residue: 1.1205 time to fit residues: 297.8018 Evaluate side-chains 222 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 31 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 152 optimal weight: 0.0570 chunk 175 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN D 267 GLN D 442 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113696 restraints weight = 56566.309| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.78 r_work: 0.3267 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17187 Z= 0.132 Angle : 0.497 5.143 23487 Z= 0.250 Chirality : 0.042 0.191 2779 Planarity : 0.004 0.039 2895 Dihedral : 7.565 88.972 2647 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.88 % Favored : 98.07 % Rotamer: Outliers : 0.70 % Allowed : 14.59 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.19), residues: 2016 helix: 2.91 (0.17), residues: 792 sheet: -0.52 (0.25), residues: 390 loop : -0.18 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 446 TYR 0.012 0.001 TYR C 213 PHE 0.011 0.001 PHE A 225 TRP 0.009 0.001 TRP C 311 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (17159) covalent geometry : angle 0.48714 / 0.25 (23409) SS BOND : bond 0.00299 / 0.16 ( 6) SS BOND : angle 1.14381 / 0.66 ( 12) hydrogen bonds : bond 0.03914 / 2.60 ( 882) hydrogen bonds : angle 3.99520 / 2.85 ( 2796) link_ALPHA1-3 : bond 0.00751 / 0.36 ( 3) link_ALPHA1-3 : angle 1.76331 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00725 / 0.36 ( 3) link_ALPHA1-6 : angle 1.90240 / 1.10 ( 9) link_BETA1-4 : bond 0.00332 / 0.20 ( 10) link_BETA1-4 : angle 1.91270 / 1.26 ( 30) link_NAG-ASN : bond 0.00214 / 0.10 ( 6) link_NAG-ASN : angle 1.65579 / 0.96 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7731 (mm-30) REVERT: A 387 LYS cc_start: 0.8548 (mmmm) cc_final: 0.7455 (mttt) REVERT: A 415 MET cc_start: 0.6610 (ptm) cc_final: 0.5890 (mmt) REVERT: C 259 VAL cc_start: 0.8137 (t) cc_final: 0.7921 (m) REVERT: C 380 LYS cc_start: 0.7598 (mtpt) cc_final: 0.7187 (mmmt) REVERT: E 44 ASN cc_start: 0.8704 (t0) cc_final: 0.8376 (t0) REVERT: E 71 GLU cc_start: 0.7175 (mp0) cc_final: 0.6920 (mp0) REVERT: E 319 MET cc_start: 0.7567 (ttm) cc_final: 0.7304 (ttm) REVERT: E 461 LEU cc_start: 0.7984 (tp) cc_final: 0.7562 (mp) REVERT: D 186 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: D 431 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7815 (mt0) REVERT: B 14 ASN cc_start: 0.8455 (t0) cc_final: 0.8236 (m-40) REVERT: B 225 ILE cc_start: 0.8548 (mt) cc_final: 0.8300 (mm) REVERT: B 272 GLN cc_start: 0.7685 (pt0) cc_final: 0.7113 (mt0) REVERT: B 286 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7026 (mtp180) REVERT: B 408 ASN cc_start: 0.8478 (m-40) cc_final: 0.7776 (m110) REVERT: B 429 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7145 (mtm180) outliers start: 13 outliers final: 10 residues processed: 224 average time/residue: 1.0718 time to fit residues: 275.8138 Evaluate side-chains 219 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 chunk 192 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 164 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN C 394 ASN E 159 GLN D 267 GLN D 442 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.141336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114365 restraints weight = 56165.875| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.78 r_work: 0.3276 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17187 Z= 0.114 Angle : 0.484 5.132 23487 Z= 0.244 Chirality : 0.042 0.200 2779 Planarity : 0.004 0.039 2895 Dihedral : 7.353 88.838 2647 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.79 % Favored : 98.16 % Rotamer: Outliers : 0.80 % Allowed : 14.54 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.19), residues: 2016 helix: 2.98 (0.17), residues: 792 sheet: -0.51 (0.25), residues: 390 loop : -0.14 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 446 TYR 0.012 0.001 TYR C 213 PHE 0.009 0.001 PHE B 439 TRP 0.009 0.001 TRP C 311 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (17159) covalent geometry : angle 0.47564 / 0.24 (23409) SS BOND : bond 0.00253 / 0.13 ( 6) SS BOND : angle 0.97495 / 0.56 ( 12) hydrogen bonds : bond 0.03826 / 2.54 ( 882) hydrogen bonds : angle 3.94413 / 2.82 ( 2796) link_ALPHA1-3 : bond 0.00732 / 0.35 ( 3) link_ALPHA1-3 : angle 1.79617 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00746 / 0.36 ( 3) link_ALPHA1-6 : angle 1.88248 / 1.09 ( 9) link_BETA1-4 : bond 0.00312 / 0.19 ( 10) link_BETA1-4 : angle 1.80421 / 1.20 ( 30) link_NAG-ASN : bond 0.00133 / 0.07 ( 6) link_NAG-ASN : angle 1.57346 / 0.91 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11593.24 seconds wall clock time: 196 minutes 29.28 seconds (11789.28 seconds total)