Starting phenix.real_space_refine on Sun Jun 15 20:44:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6z_28893/06_2025/8f6z_28893.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6z_28893/06_2025/8f6z_28893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6z_28893/06_2025/8f6z_28893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6z_28893/06_2025/8f6z_28893.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6z_28893/06_2025/8f6z_28893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6z_28893/06_2025/8f6z_28893.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 85 5.16 5 C 11129 2.51 5 N 2640 2.21 5 O 3138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16997 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3140 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3456 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3151 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 367} Chain breaks: 1 Chain: "E" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 386} 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: "J" 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: "K" 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: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'CLR': 1, 'SCK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'DD9': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'CLR': 1, 'POV': 1, 'SCK': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1 CLR A 502 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 502 " occ=0.80 residue: pdb=" N POV B 602 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 602 " occ=0.75 residue: pdb=" C1 CLR C 501 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR C 501 " occ=0.89 residue: pdb=" C1 CLR D 503 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 503 " occ=0.75 Time building chain proxies: 11.58, per 1000 atoms: 0.68 Number of scatterers: 16997 At special positions: 0 Unit cell: (99.4542, 111.218, 164.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 5 15.00 O 3138 8.00 N 2640 7.00 C 11129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.02 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.04 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " 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 ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 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 I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG B 601 " - " ASN B 70 " " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN B 208 " " NAG I 1 " - " ASN C 141 " " NAG J 1 " - " ASN D 141 " " NAG K 1 " - " ASN E 141 " Time building additional restraints: 5.53 Conformation dependent library (CDL) restraints added in 2.2 seconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 43.7% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.563A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.232A pdb=" N GLY A 73 " --> pdb=" O ALA 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 212 through 218 Processing helix chain 'A' and resid 218 through 235 removed outlier: 4.053A pdb=" N THR A 229 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) 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 removed outlier: 3.726A pdb=" N ILE A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 371 through 426 removed outlier: 3.507A pdb=" N ALA A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.713A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.619A pdb=" N GLY B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 323 through 332 removed outlier: 3.656A pdb=" N GLU B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 removed outlier: 4.196A pdb=" N ARG B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 478 removed outlier: 3.653A pdb=" N SER B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Proline residue: B 463 - end of helix removed outlier: 3.811A pdb=" N ASN B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.091A pdb=" N GLU C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.532A pdb=" N VAL C 85 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 180 removed outlier: 3.900A pdb=" N PHE C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 217 through 238 removed outlier: 4.639A pdb=" N ILE C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 247 through 267 Processing helix chain 'C' and resid 278 through 306 Processing helix chain 'C' and resid 315 through 324 removed outlier: 3.585A pdb=" N GLU C 324 " --> pdb=" O GLN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 4.163A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 460 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.037A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 218 through 230 removed outlier: 4.006A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 236 through 240 Processing helix chain 'D' and resid 241 through 262 removed outlier: 3.834A pdb=" N GLU D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 317 Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 371 through 426 removed outlier: 3.613A pdb=" N PHE D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 4.180A pdb=" N ARG E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 3.993A pdb=" N GLU E 73 " --> pdb=" O SER 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 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 250 through 271 removed outlier: 3.628A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.615A pdb=" N PHE E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 472 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.130A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.130A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 35 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ILE A 61 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 31 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.716A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 removed outlier: 4.602A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 123 through 129 removed outlier: 6.808A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ILE B 178 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 37 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 4.686A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 4.686A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.868A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN C 53 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU C 40 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N PHE C 55 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C 38 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN C 57 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR C 36 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA C 59 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY C 34 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR C 61 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ARG C 32 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 127 removed outlier: 6.807A pdb=" N ASN C 53 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU C 40 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N PHE C 55 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C 38 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN C 57 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR C 36 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA C 59 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY C 34 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR C 61 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ARG C 32 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N VAL C 174 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU C 35 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.150A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.150A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N TYR C 204 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG C 198 " --> pdb=" O TYR C 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.216A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.216A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE D 49 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL D 43 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU D 51 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG D 55 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU D 37 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG D 57 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU D 35 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLN D 59 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL D 33 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ILE D 61 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE D 31 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.772A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TYR D 198 " --> pdb=" O TRP D 187 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP D 187 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP D 200 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS D 185 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR D 202 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY D 183 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS D 204 " --> pdb=" O TYR D 181 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR D 181 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE D 206 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.822A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.822A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.232A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.232A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 162 through 163 921 hydrogen bonds defined for protein. 2646 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: 5.86 Time building geometry restraints manager: 6.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2644 1.31 - 1.44: 4786 1.44 - 1.58: 9853 1.58 - 1.71: 13 1.71 - 1.84: 139 Bond restraints: 17435 Sorted by residual: bond pdb=" C31 POV B 602 " pdb=" O31 POV B 602 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C31 POV C 503 " pdb=" O31 POV C 503 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C31 POV C 502 " pdb=" O31 POV C 502 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C21 POV C 503 " pdb=" O21 POV C 503 " ideal model delta sigma weight residual 1.330 1.401 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C21 POV B 602 " pdb=" O21 POV B 602 " ideal model delta sigma weight residual 1.330 1.400 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 17430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 23384 2.62 - 5.25: 328 5.25 - 7.87: 47 7.87 - 10.50: 12 10.50 - 13.12: 10 Bond angle restraints: 23781 Sorted by residual: angle pdb=" O11 POV E 502 " pdb=" P POV E 502 " pdb=" O12 POV E 502 " ideal model delta sigma weight residual 97.67 110.79 -13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" O11 POV C 502 " pdb=" P POV C 502 " pdb=" O12 POV C 502 " ideal model delta sigma weight residual 97.67 109.91 -12.24 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O13 POV C 502 " pdb=" P POV C 502 " pdb=" O14 POV C 502 " ideal model delta sigma weight residual 121.11 109.06 12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O11 POV C 503 " pdb=" P POV C 503 " pdb=" O12 POV C 503 " ideal model delta sigma weight residual 97.67 109.61 -11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O11 POV B 602 " pdb=" P POV B 602 " pdb=" O12 POV B 602 " ideal model delta sigma weight residual 97.67 109.52 -11.85 3.00e+00 1.11e-01 1.56e+01 ... (remaining 23776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.83: 10485 29.83 - 59.67: 281 59.67 - 89.50: 67 89.50 - 119.34: 20 119.34 - 149.17: 2 Dihedral angle restraints: 10855 sinusoidal: 4875 harmonic: 5980 Sorted by residual: dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU B 418 " pdb=" C GLU B 418 " pdb=" N ILE B 419 " pdb=" CA ILE B 419 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 10852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2353 0.059 - 0.118: 409 0.118 - 0.176: 44 0.176 - 0.235: 2 0.235 - 0.294: 7 Chirality restraints: 2815 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2812 not shown) Planarity restraints: 2881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 483 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO E 484 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 484 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 484 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 223 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" C ILE E 223 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE E 223 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE E 224 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 393 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C SER A 393 " -0.034 2.00e-02 2.50e+03 pdb=" O SER A 393 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 394 " 0.011 2.00e-02 2.50e+03 ... (remaining 2878 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 91 2.51 - 3.10: 12885 3.10 - 3.70: 26834 3.70 - 4.30: 40888 4.30 - 4.90: 67704 Nonbonded interactions: 148402 Sorted by model distance: nonbonded pdb=" OG SER B 244 " pdb=" OG1 THR B 462 " model vdw 1.907 3.040 nonbonded pdb=" OD1 ASN B 98 " pdb=" OG SER B 129 " model vdw 2.032 3.040 nonbonded pdb=" OD2 ASP A 152 " pdb=" OG1 THR A 154 " model vdw 2.070 3.040 nonbonded pdb=" OG SER A 82 " pdb=" O THR A 106 " model vdw 2.085 3.040 nonbonded pdb=" OD2 ASP D 138 " pdb=" NE2 GLN D 140 " model vdw 2.107 3.120 ... (remaining 148397 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 426 or resid 501)) selection = (chain 'D' and (resid 1 through 330 or resid 370 through 426 or resid 501)) } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.180 Set scattering table: 0.270 Process input model: 43.800 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 17468 Z= 0.316 Angle : 0.812 13.119 23873 Z= 0.371 Chirality : 0.047 0.294 2815 Planarity : 0.004 0.056 2873 Dihedral : 15.710 149.173 6940 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 1995 helix: 1.84 (0.19), residues: 756 sheet: -0.92 (0.24), residues: 389 loop : -0.68 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 118 HIS 0.004 0.001 HIS B 103 PHE 0.015 0.002 PHE C 12 TYR 0.015 0.002 TYR C 223 ARG 0.009 0.001 ARG E 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00940 ( 8) link_NAG-ASN : angle 2.83956 ( 24) link_ALPHA1-6 : bond 0.00556 ( 7) link_ALPHA1-6 : angle 1.77668 ( 21) link_BETA1-4 : bond 0.00572 ( 11) link_BETA1-4 : angle 2.01627 ( 33) hydrogen bonds : bond 0.12008 ( 846) hydrogen bonds : angle 6.10941 ( 2646) SS BOND : bond 0.00769 ( 7) SS BOND : angle 2.11828 ( 14) covalent geometry : bond 0.00676 (17435) covalent geometry : angle 0.80174 (23781) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 1.5888 time to fit residues: 160.7729 Evaluate side-chains 74 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 179 optimal weight: 0.0170 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS B 20 HIS B 276 GLN D 204 HIS D 385 HIS E 172 HIS ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN E 437 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.066033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.050454 restraints weight = 38853.764| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.79 r_work: 0.2584 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17468 Z= 0.138 Angle : 0.567 6.616 23873 Z= 0.282 Chirality : 0.044 0.177 2815 Planarity : 0.004 0.041 2873 Dihedral : 11.865 128.591 3031 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.86 % Allowed : 4.51 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1995 helix: 2.29 (0.18), residues: 773 sheet: -0.78 (0.24), residues: 388 loop : -0.47 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.003 0.001 HIS B 60 PHE 0.012 0.001 PHE E 467 TYR 0.018 0.001 TYR E 117 ARG 0.010 0.001 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 8) link_NAG-ASN : angle 2.18359 ( 24) link_ALPHA1-6 : bond 0.00949 ( 7) link_ALPHA1-6 : angle 1.86582 ( 21) link_BETA1-4 : bond 0.00599 ( 11) link_BETA1-4 : angle 2.05337 ( 33) hydrogen bonds : bond 0.04144 ( 846) hydrogen bonds : angle 4.48100 ( 2646) SS BOND : bond 0.00690 ( 7) SS BOND : angle 1.80334 ( 14) covalent geometry : bond 0.00305 (17435) covalent geometry : angle 0.55393 (23781) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8067 (t0) cc_final: 0.7519 (t0) REVERT: A 373 LYS cc_start: 0.6655 (mmtt) cc_final: 0.6437 (mmtt) REVERT: C 168 ARG cc_start: 0.8800 (ptp-110) cc_final: 0.8317 (ptm-80) REVERT: D 171 MET cc_start: 0.8130 (mtp) cc_final: 0.7723 (ptp) REVERT: D 208 GLN cc_start: 0.8669 (tp40) cc_final: 0.8441 (tp40) REVERT: D 324 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7744 (mtp) REVERT: D 404 MET cc_start: 0.8636 (tmm) cc_final: 0.8220 (tmt) REVERT: E 116 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8808 (mmm) outliers start: 16 outliers final: 6 residues processed: 92 average time/residue: 2.0203 time to fit residues: 209.1061 Evaluate side-chains 81 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain E residue 116 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 32 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 276 GLN D 3 HIS D 310 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.050101 restraints weight = 39156.927| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.80 r_work: 0.2579 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17468 Z= 0.146 Angle : 0.518 7.177 23873 Z= 0.258 Chirality : 0.043 0.164 2815 Planarity : 0.003 0.037 2873 Dihedral : 10.183 127.398 3031 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.02 % Allowed : 5.96 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1995 helix: 2.54 (0.18), residues: 777 sheet: -0.77 (0.24), residues: 380 loop : -0.42 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 187 HIS 0.003 0.001 HIS B 60 PHE 0.012 0.001 PHE E 467 TYR 0.012 0.001 TYR B 439 ARG 0.003 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 8) link_NAG-ASN : angle 2.04123 ( 24) link_ALPHA1-6 : bond 0.00699 ( 7) link_ALPHA1-6 : angle 1.84995 ( 21) link_BETA1-4 : bond 0.00457 ( 11) link_BETA1-4 : angle 1.91801 ( 33) hydrogen bonds : bond 0.03847 ( 846) hydrogen bonds : angle 4.17604 ( 2646) SS BOND : bond 0.01231 ( 7) SS BOND : angle 1.83846 ( 14) covalent geometry : bond 0.00331 (17435) covalent geometry : angle 0.50479 (23781) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 2.455 Fit side-chains REVERT: A 373 LYS cc_start: 0.6731 (mmtt) cc_final: 0.6493 (mmtt) REVERT: C 168 ARG cc_start: 0.8799 (ptp-110) cc_final: 0.8275 (ptm-80) REVERT: D 117 MET cc_start: 0.8988 (tpt) cc_final: 0.8745 (tpt) REVERT: D 171 MET cc_start: 0.8050 (mtp) cc_final: 0.7635 (ptp) REVERT: D 208 GLN cc_start: 0.8673 (tp40) cc_final: 0.8471 (tp40) REVERT: D 404 MET cc_start: 0.8669 (tmm) cc_final: 0.8097 (tmt) REVERT: E 116 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8830 (mmm) outliers start: 19 outliers final: 4 residues processed: 86 average time/residue: 1.6610 time to fit residues: 160.2381 Evaluate side-chains 78 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 116 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 176 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 chunk 22 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 72 optimal weight: 8.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN B 276 GLN D 48 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.066685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.051232 restraints weight = 38798.754| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.80 r_work: 0.2615 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17468 Z= 0.110 Angle : 0.489 6.481 23873 Z= 0.244 Chirality : 0.042 0.193 2815 Planarity : 0.003 0.036 2873 Dihedral : 9.117 122.248 3031 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.61 % Allowed : 6.39 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1995 helix: 2.72 (0.18), residues: 778 sheet: -0.69 (0.24), residues: 401 loop : -0.27 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.003 0.000 HIS B 60 PHE 0.011 0.001 PHE E 467 TYR 0.011 0.001 TYR B 439 ARG 0.002 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 8) link_NAG-ASN : angle 1.79198 ( 24) link_ALPHA1-6 : bond 0.00815 ( 7) link_ALPHA1-6 : angle 1.78724 ( 21) link_BETA1-4 : bond 0.00472 ( 11) link_BETA1-4 : angle 1.68582 ( 33) hydrogen bonds : bond 0.03503 ( 846) hydrogen bonds : angle 3.94227 ( 2646) SS BOND : bond 0.00887 ( 7) SS BOND : angle 1.70484 ( 14) covalent geometry : bond 0.00243 (17435) covalent geometry : angle 0.47737 (23781) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 2.669 Fit side-chains REVERT: A 373 LYS cc_start: 0.6700 (mmtt) cc_final: 0.6294 (mmtt) REVERT: A 397 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8373 (mp0) REVERT: C 436 ASP cc_start: 0.8216 (t0) cc_final: 0.7991 (t0) REVERT: D 48 GLN cc_start: 0.9068 (mt0) cc_final: 0.8738 (mt0) REVERT: D 171 MET cc_start: 0.7930 (mtp) cc_final: 0.7610 (ptp) REVERT: D 208 GLN cc_start: 0.8671 (tp40) cc_final: 0.8426 (tp40) REVERT: E 116 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8815 (mmm) outliers start: 30 outliers final: 7 residues processed: 100 average time/residue: 1.7412 time to fit residues: 194.4508 Evaluate side-chains 88 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 49 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 0.0000 chunk 86 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN B 276 GLN D 310 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.051238 restraints weight = 39647.721| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.82 r_work: 0.2622 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 17468 Z= 0.118 Angle : 0.512 15.598 23873 Z= 0.251 Chirality : 0.042 0.179 2815 Planarity : 0.003 0.038 2873 Dihedral : 8.901 121.881 3031 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.34 % Allowed : 7.19 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 1995 helix: 2.78 (0.18), residues: 778 sheet: -0.66 (0.24), residues: 400 loop : -0.21 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.003 0.000 HIS B 60 PHE 0.011 0.001 PHE E 467 TYR 0.012 0.001 TYR B 439 ARG 0.009 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 8) link_NAG-ASN : angle 1.79064 ( 24) link_ALPHA1-6 : bond 0.00743 ( 7) link_ALPHA1-6 : angle 1.75407 ( 21) link_BETA1-4 : bond 0.00461 ( 11) link_BETA1-4 : angle 1.67960 ( 33) hydrogen bonds : bond 0.03443 ( 846) hydrogen bonds : angle 3.88181 ( 2646) SS BOND : bond 0.01020 ( 7) SS BOND : angle 3.51259 ( 14) covalent geometry : bond 0.00273 (17435) covalent geometry : angle 0.49616 (23781) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 2.154 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.6631 (mmtt) cc_final: 0.6163 (mmtt) REVERT: C 168 ARG cc_start: 0.8758 (ptp-110) cc_final: 0.8291 (ptm-80) REVERT: C 436 ASP cc_start: 0.8217 (t0) cc_final: 0.7973 (t0) REVERT: D 48 GLN cc_start: 0.9046 (mt0) cc_final: 0.8650 (mt0) REVERT: D 171 MET cc_start: 0.7944 (mtp) cc_final: 0.7627 (ptp) REVERT: D 208 GLN cc_start: 0.8681 (tp40) cc_final: 0.8437 (tp40) REVERT: E 116 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8827 (mmm) outliers start: 25 outliers final: 9 residues processed: 97 average time/residue: 1.4406 time to fit residues: 158.5331 Evaluate side-chains 89 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 97 optimal weight: 0.0370 chunk 99 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN C 95 ASN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.063747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.048181 restraints weight = 39845.375| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.80 r_work: 0.2542 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 17468 Z= 0.254 Angle : 0.580 16.196 23873 Z= 0.284 Chirality : 0.044 0.194 2815 Planarity : 0.003 0.038 2873 Dihedral : 8.958 123.447 3031 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.18 % Allowed : 8.16 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.19), residues: 1995 helix: 2.66 (0.18), residues: 777 sheet: -0.66 (0.24), residues: 399 loop : -0.25 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 149 HIS 0.005 0.001 HIS B 60 PHE 0.013 0.001 PHE E 467 TYR 0.015 0.001 TYR B 439 ARG 0.008 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 8) link_NAG-ASN : angle 2.08186 ( 24) link_ALPHA1-6 : bond 0.00592 ( 7) link_ALPHA1-6 : angle 1.86336 ( 21) link_BETA1-4 : bond 0.00359 ( 11) link_BETA1-4 : angle 1.95852 ( 33) hydrogen bonds : bond 0.03849 ( 846) hydrogen bonds : angle 4.08465 ( 2646) SS BOND : bond 0.00943 ( 7) SS BOND : angle 3.63390 ( 14) covalent geometry : bond 0.00592 (17435) covalent geometry : angle 0.56334 (23781) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: A 282 MET cc_start: 0.8566 (ttm) cc_final: 0.8356 (mtp) REVERT: A 373 LYS cc_start: 0.6558 (mmtt) cc_final: 0.6094 (mmtt) REVERT: A 397 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: B 95 GLN cc_start: 0.9190 (tt0) cc_final: 0.8980 (tt0) REVERT: C 168 ARG cc_start: 0.8751 (ptp-110) cc_final: 0.8230 (ptm-80) REVERT: C 436 ASP cc_start: 0.8252 (t0) cc_final: 0.8006 (t0) REVERT: D 171 MET cc_start: 0.7972 (mtp) cc_final: 0.7559 (ptp) REVERT: D 208 GLN cc_start: 0.8704 (tp40) cc_final: 0.8473 (tp40) REVERT: D 407 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8266 (m-30) outliers start: 22 outliers final: 12 residues processed: 92 average time/residue: 1.8315 time to fit residues: 188.5575 Evaluate side-chains 89 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 100 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN D 310 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.064617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.049164 restraints weight = 39448.642| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.79 r_work: 0.2566 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 17468 Z= 0.173 Angle : 0.535 16.320 23873 Z= 0.262 Chirality : 0.042 0.181 2815 Planarity : 0.003 0.036 2873 Dihedral : 8.662 122.322 3031 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.29 % Allowed : 8.16 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.19), residues: 1995 helix: 2.72 (0.18), residues: 777 sheet: -0.74 (0.24), residues: 401 loop : -0.25 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.004 0.001 HIS B 60 PHE 0.012 0.001 PHE E 467 TYR 0.013 0.001 TYR B 439 ARG 0.006 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 8) link_NAG-ASN : angle 1.90632 ( 24) link_ALPHA1-6 : bond 0.00716 ( 7) link_ALPHA1-6 : angle 1.77377 ( 21) link_BETA1-4 : bond 0.00397 ( 11) link_BETA1-4 : angle 1.70827 ( 33) hydrogen bonds : bond 0.03632 ( 846) hydrogen bonds : angle 3.99388 ( 2646) SS BOND : bond 0.00955 ( 7) SS BOND : angle 3.34945 ( 14) covalent geometry : bond 0.00399 (17435) covalent geometry : angle 0.52013 (23781) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 1.914 Fit side-chains revert: symmetry clash REVERT: A 282 MET cc_start: 0.8597 (ttm) cc_final: 0.8390 (mtp) REVERT: A 373 LYS cc_start: 0.6546 (mmtt) cc_final: 0.6081 (mmtt) REVERT: B 95 GLN cc_start: 0.9172 (tt0) cc_final: 0.8951 (tt0) REVERT: C 168 ARG cc_start: 0.8753 (ptp-110) cc_final: 0.8259 (ptm-80) REVERT: C 436 ASP cc_start: 0.8245 (t0) cc_final: 0.8003 (t0) REVERT: D 171 MET cc_start: 0.7921 (mtp) cc_final: 0.7453 (ptp) REVERT: D 208 GLN cc_start: 0.8687 (tp40) cc_final: 0.8418 (tp40) REVERT: D 407 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8284 (m-30) REVERT: E 323 HIS cc_start: 0.9164 (t-90) cc_final: 0.8706 (t-90) outliers start: 24 outliers final: 11 residues processed: 95 average time/residue: 1.5149 time to fit residues: 160.8951 Evaluate side-chains 89 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 43 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 175 optimal weight: 0.2980 chunk 88 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 58 optimal weight: 0.0070 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS B 276 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.050153 restraints weight = 39230.459| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.81 r_work: 0.2596 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 17468 Z= 0.125 Angle : 0.512 16.547 23873 Z= 0.253 Chirality : 0.042 0.172 2815 Planarity : 0.003 0.036 2873 Dihedral : 8.373 120.671 3031 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.07 % Allowed : 8.80 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1995 helix: 2.77 (0.18), residues: 779 sheet: -0.71 (0.24), residues: 397 loop : -0.21 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.006 0.001 HIS A 408 PHE 0.012 0.001 PHE E 467 TYR 0.012 0.001 TYR B 439 ARG 0.006 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 8) link_NAG-ASN : angle 1.75141 ( 24) link_ALPHA1-6 : bond 0.00724 ( 7) link_ALPHA1-6 : angle 1.69373 ( 21) link_BETA1-4 : bond 0.00438 ( 11) link_BETA1-4 : angle 1.61123 ( 33) hydrogen bonds : bond 0.03447 ( 846) hydrogen bonds : angle 3.90197 ( 2646) SS BOND : bond 0.00949 ( 7) SS BOND : angle 3.18762 ( 14) covalent geometry : bond 0.00283 (17435) covalent geometry : angle 0.49755 (23781) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 2.022 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8082 (t0) cc_final: 0.7559 (t0) REVERT: A 282 MET cc_start: 0.8634 (ttm) cc_final: 0.8432 (mtp) REVERT: A 373 LYS cc_start: 0.6437 (mmtt) cc_final: 0.5992 (mmtt) REVERT: A 404 MET cc_start: 0.7614 (tmt) cc_final: 0.7339 (tmt) REVERT: A 416 LEU cc_start: 0.8273 (tt) cc_final: 0.8001 (mp) REVERT: B 95 GLN cc_start: 0.9146 (tt0) cc_final: 0.8914 (tt0) REVERT: C 50 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8892 (ttm) REVERT: C 168 ARG cc_start: 0.8755 (ptp-110) cc_final: 0.8310 (ptm-80) REVERT: C 436 ASP cc_start: 0.8251 (t0) cc_final: 0.7984 (t0) REVERT: D 48 GLN cc_start: 0.9094 (mt0) cc_final: 0.8774 (mt0) REVERT: D 171 MET cc_start: 0.7889 (mtp) cc_final: 0.7493 (ptp) REVERT: D 208 GLN cc_start: 0.8689 (tp40) cc_final: 0.8419 (tp40) REVERT: D 407 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8221 (m-30) REVERT: E 323 HIS cc_start: 0.9133 (t-90) cc_final: 0.8752 (t-90) outliers start: 20 outliers final: 13 residues processed: 94 average time/residue: 1.4059 time to fit residues: 147.8505 Evaluate side-chains 94 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 186 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS B 276 GLN D 310 GLN D 322 ASN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.065731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.050274 restraints weight = 39359.818| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.84 r_work: 0.2599 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 17468 Z= 0.129 Angle : 0.514 16.713 23873 Z= 0.252 Chirality : 0.042 0.167 2815 Planarity : 0.003 0.036 2873 Dihedral : 8.177 119.381 3031 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.02 % Allowed : 9.07 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 1995 helix: 2.79 (0.18), residues: 779 sheet: -0.67 (0.24), residues: 396 loop : -0.18 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.004 0.001 HIS B 60 PHE 0.012 0.001 PHE E 467 TYR 0.012 0.001 TYR B 439 ARG 0.005 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 8) link_NAG-ASN : angle 1.77075 ( 24) link_ALPHA1-6 : bond 0.00701 ( 7) link_ALPHA1-6 : angle 1.65687 ( 21) link_BETA1-4 : bond 0.00417 ( 11) link_BETA1-4 : angle 1.59344 ( 33) hydrogen bonds : bond 0.03401 ( 846) hydrogen bonds : angle 3.85847 ( 2646) SS BOND : bond 0.00919 ( 7) SS BOND : angle 3.15537 ( 14) covalent geometry : bond 0.00294 (17435) covalent geometry : angle 0.50058 (23781) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 2.044 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8136 (t0) cc_final: 0.7591 (t0) REVERT: A 373 LYS cc_start: 0.6432 (mmtt) cc_final: 0.5989 (mmtt) REVERT: A 386 MET cc_start: 0.8458 (mtp) cc_final: 0.8229 (ttm) REVERT: B 95 GLN cc_start: 0.9150 (tt0) cc_final: 0.8913 (tt0) REVERT: C 50 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8893 (ttm) REVERT: C 168 ARG cc_start: 0.8753 (ptp-110) cc_final: 0.8306 (ptm-80) REVERT: C 436 ASP cc_start: 0.8255 (t0) cc_final: 0.7990 (t0) REVERT: C 468 PHE cc_start: 0.8879 (m-80) cc_final: 0.8228 (m-10) REVERT: D 48 GLN cc_start: 0.9092 (mt0) cc_final: 0.8780 (mt0) REVERT: D 171 MET cc_start: 0.7919 (mtp) cc_final: 0.7527 (ptp) REVERT: D 208 GLN cc_start: 0.8693 (tp40) cc_final: 0.8422 (tp40) REVERT: D 326 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8103 (p90) REVERT: D 407 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: E 323 HIS cc_start: 0.9131 (t-90) cc_final: 0.8775 (t-90) outliers start: 19 outliers final: 15 residues processed: 95 average time/residue: 1.4338 time to fit residues: 153.2161 Evaluate side-chains 97 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 187 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.065804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.050350 restraints weight = 39318.487| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.81 r_work: 0.2602 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 17468 Z= 0.129 Angle : 0.513 17.248 23873 Z= 0.252 Chirality : 0.042 0.163 2815 Planarity : 0.003 0.037 2873 Dihedral : 8.030 117.919 3031 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.02 % Allowed : 9.02 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 1995 helix: 2.83 (0.18), residues: 779 sheet: -0.67 (0.24), residues: 397 loop : -0.15 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.004 0.001 HIS B 60 PHE 0.012 0.001 PHE E 467 TYR 0.012 0.001 TYR B 439 ARG 0.005 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 8) link_NAG-ASN : angle 1.73859 ( 24) link_ALPHA1-6 : bond 0.00687 ( 7) link_ALPHA1-6 : angle 1.62133 ( 21) link_BETA1-4 : bond 0.00423 ( 11) link_BETA1-4 : angle 1.56802 ( 33) hydrogen bonds : bond 0.03367 ( 846) hydrogen bonds : angle 3.83873 ( 2646) SS BOND : bond 0.00922 ( 7) SS BOND : angle 3.13400 ( 14) covalent geometry : bond 0.00296 (17435) covalent geometry : angle 0.49920 (23781) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 1.899 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8192 (t0) cc_final: 0.7613 (t0) REVERT: A 373 LYS cc_start: 0.6404 (mmtt) cc_final: 0.5976 (mmtt) REVERT: A 386 MET cc_start: 0.8451 (mtp) cc_final: 0.8229 (ttm) REVERT: A 416 LEU cc_start: 0.8259 (tt) cc_final: 0.7987 (mp) REVERT: B 95 GLN cc_start: 0.9144 (tt0) cc_final: 0.8917 (tt0) REVERT: C 50 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8884 (ttm) REVERT: C 168 ARG cc_start: 0.8751 (ptp-110) cc_final: 0.8305 (ptm-80) REVERT: C 436 ASP cc_start: 0.8253 (t0) cc_final: 0.7993 (t0) REVERT: C 468 PHE cc_start: 0.8878 (m-80) cc_final: 0.8235 (m-10) REVERT: D 48 GLN cc_start: 0.9094 (mt0) cc_final: 0.8787 (mt0) REVERT: D 171 MET cc_start: 0.7920 (mtp) cc_final: 0.7532 (ptp) REVERT: D 208 GLN cc_start: 0.8691 (tp40) cc_final: 0.8434 (tp40) REVERT: D 407 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8187 (t0) REVERT: E 323 HIS cc_start: 0.9114 (t-90) cc_final: 0.8762 (t-90) outliers start: 19 outliers final: 15 residues processed: 92 average time/residue: 1.5004 time to fit residues: 153.9627 Evaluate side-chains 96 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 195 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 58 optimal weight: 0.0670 chunk 125 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS B 276 GLN B 437 ASN D 310 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.066273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.050899 restraints weight = 39126.174| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.80 r_work: 0.2617 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 17468 Z= 0.116 Angle : 0.502 17.329 23873 Z= 0.247 Chirality : 0.041 0.157 2815 Planarity : 0.003 0.037 2873 Dihedral : 7.815 115.634 3031 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.13 % Allowed : 9.07 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.19), residues: 1995 helix: 2.88 (0.18), residues: 779 sheet: -0.65 (0.24), residues: 393 loop : -0.13 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.003 0.000 HIS B 60 PHE 0.011 0.001 PHE E 467 TYR 0.011 0.001 TYR B 439 ARG 0.005 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 8) link_NAG-ASN : angle 1.70410 ( 24) link_ALPHA1-6 : bond 0.00672 ( 7) link_ALPHA1-6 : angle 1.55997 ( 21) link_BETA1-4 : bond 0.00439 ( 11) link_BETA1-4 : angle 1.52578 ( 33) hydrogen bonds : bond 0.03278 ( 846) hydrogen bonds : angle 3.79375 ( 2646) SS BOND : bond 0.00909 ( 7) SS BOND : angle 3.07908 ( 14) covalent geometry : bond 0.00264 (17435) covalent geometry : angle 0.48937 (23781) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9755.08 seconds wall clock time: 173 minutes 58.21 seconds (10438.21 seconds total)