Starting phenix.real_space_refine on Sun Aug 24 06:59:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6y_28892/08_2025/8f6y_28892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6y_28892/08_2025/8f6y_28892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6y_28892/08_2025/8f6y_28892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6y_28892/08_2025/8f6y_28892.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6y_28892/08_2025/8f6y_28892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6y_28892/08_2025/8f6y_28892.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 6 5.49 5 S 85 5.16 5 C 11180 2.51 5 N 2649 2.21 5 O 3133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17053 Number of models: 1 Model: "" Number of chains: 18 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: 3463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3463 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 398} Chain breaks: 1 Chain: "C" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3315 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 384} 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: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3346 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 389} 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: 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'CHT': 1, 'CLR': 1, 'V8D': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 97 Unusual residues: {'CHT': 1, 'CLR': 1, 'DD9': 1, 'POV': 1, 'V8D': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'NAG': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} 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} Time building chain proxies: 4.33, per 1000 atoms: 0.25 Number of scatterers: 17053 At special positions: 0 Unit cell: (109.824, 139.392, 156.288, 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 6 15.00 O 3133 8.00 N 2649 7.00 C 11180 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=2.01 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 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 I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 601 " - " ASN B 208 " " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN D 141 " " NAG J 1 " - " ASN E 141 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 689.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3908 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 20 sheets defined 43.7% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.844A 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: 4.065A 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 227 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.949A pdb=" N TYR A 234 " --> pdb=" O GLY A 230 " (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 319 removed outlier: 3.845A pdb=" N ILE A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 371 through 426 removed outlier: 3.506A pdb=" N PHE A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 4.028A pdb=" N ARG B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 68 removed outlier: 3.816A pdb=" N THR B 68 " --> pdb=" O HIS B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.701A pdb=" N CYS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.792A 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 255 through 277 Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.933A pdb=" N ARG B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 476 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.580A pdb=" N GLU C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.652A pdb=" N VAL C 85 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.925A pdb=" N PHE C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 238 removed outlier: 4.765A 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 242 through 246 removed outlier: 3.652A pdb=" N GLY C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) 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: 3.799A pdb=" N GLU C 324 " --> pdb=" O GLN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.989A 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: 4.096A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 218 through 229 Processing helix chain 'D' and resid 230 through 235 removed outlier: 3.584A pdb=" N PHE D 233 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 240 Processing helix chain 'D' and resid 241 through 262 removed outlier: 3.562A 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 318 Processing helix chain 'D' and resid 319 through 324 removed outlier: 3.596A pdb=" N VAL D 323 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET D 324 " --> pdb=" O ILE D 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 319 through 324' Processing helix chain 'D' and resid 371 through 426 Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.528A pdb=" N LEU E 7 " --> pdb=" O GLU E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.042A 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 242 Processing helix chain 'E' and resid 250 through 272 Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 327 removed outlier: 3.615A pdb=" N LYS E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 333 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: 4.230A 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: 4.230A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE A 49 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER A 42 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.820A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 205 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.618A 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 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 6.254A pdb=" N THR B 51 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU B 45 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 53 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP B 57 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU B 39 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP B 59 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU B 37 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ALA B 61 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU B 35 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N TYR B 63 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE B 33 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASP B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 33 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.042A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.792A 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: 5.042A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.075A 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: 3.710A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.710A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU C 49 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 42 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.704A 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 Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 81 removed outlier: 4.281A 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 81 removed outlier: 4.281A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE D 49 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER D 42 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.719A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 205 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.757A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 121 through 127 removed outlier: 7.187A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N HIS E 172 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU E 35 " --> pdb=" O HIS E 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.225A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.867A 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: 5.225A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.725A 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 163 930 hydrogen bonds defined for protein. 2694 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: 2.83 Time building geometry restraints manager: 2.25 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: 2648 1.31 - 1.45: 4826 1.45 - 1.58: 9869 1.58 - 1.71: 12 1.71 - 1.85: 139 Bond restraints: 17494 Sorted by residual: bond pdb=" C SER D 226 " pdb=" N PHE D 227 " ideal model delta sigma weight residual 1.335 1.386 -0.051 1.38e-02 5.25e+03 1.38e+01 bond pdb=" C PHE A 227 " pdb=" N LEU A 228 " ideal model delta sigma weight residual 1.332 1.386 -0.055 1.52e-02 4.33e+03 1.29e+01 bond pdb=" N POV B 602 " pdb=" C12 POV B 602 " ideal model delta sigma weight residual 1.508 1.446 0.062 2.00e-02 2.50e+03 9.76e+00 bond pdb=" N POV E 503 " pdb=" C12 POV E 503 " ideal model delta sigma weight residual 1.508 1.449 0.059 2.00e-02 2.50e+03 8.57e+00 bond pdb=" N POV E 502 " pdb=" C12 POV E 502 " ideal model delta sigma weight residual 1.508 1.450 0.058 2.00e-02 2.50e+03 8.29e+00 ... (remaining 17489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 23414 2.40 - 4.80: 376 4.80 - 7.21: 46 7.21 - 9.61: 7 9.61 - 12.01: 12 Bond angle restraints: 23855 Sorted by residual: angle pdb=" O13 POV C 502 " pdb=" P POV C 502 " pdb=" O14 POV C 502 " ideal model delta sigma weight residual 121.11 109.10 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O13 POV E 503 " pdb=" P POV E 503 " pdb=" O14 POV E 503 " ideal model delta sigma weight residual 121.11 109.12 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O13 POV D 604 " pdb=" P POV D 604 " pdb=" O14 POV D 604 " ideal model delta sigma weight residual 121.11 109.12 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O11 POV C 501 " pdb=" P POV C 501 " pdb=" O12 POV C 501 " ideal model delta sigma weight residual 97.67 109.55 -11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O11 POV C 502 " pdb=" P POV C 502 " pdb=" O12 POV C 502 " ideal model delta sigma weight residual 97.67 109.49 -11.82 3.00e+00 1.11e-01 1.55e+01 ... (remaining 23850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.29: 10508 31.29 - 62.58: 262 62.58 - 93.87: 56 93.87 - 125.16: 17 125.16 - 156.45: 2 Dihedral angle restraints: 10845 sinusoidal: 4843 harmonic: 6002 Sorted by residual: dihedral pdb=" CA CYS D 142 " pdb=" C CYS D 142 " pdb=" N THR D 143 " pdb=" CA THR D 143 " ideal model delta harmonic sigma weight residual 180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+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 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 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 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 10842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2673 0.103 - 0.207: 127 0.207 - 0.310: 7 0.310 - 0.414: 1 0.414 - 0.517: 1 Chirality restraints: 2809 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.96e+01 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.41e+01 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 208 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.68e+00 ... (remaining 2806 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 141 " 0.028 2.00e-02 2.50e+03 2.87e-02 1.03e+01 pdb=" CG ASN C 141 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 141 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 141 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 V8D D 601 " -0.027 2.00e-02 2.50e+03 2.30e-02 9.27e+00 pdb=" C08 V8D D 601 " -0.011 2.00e-02 2.50e+03 pdb=" C09 V8D D 601 " 0.033 2.00e-02 2.50e+03 pdb=" C12 V8D D 601 " -0.031 2.00e-02 2.50e+03 pdb=" C13 V8D D 601 " 0.026 2.00e-02 2.50e+03 pdb=" N03 V8D D 601 " 0.011 2.00e-02 2.50e+03 pdb=" N04 V8D D 601 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.024 2.00e-02 2.50e+03 2.00e-02 5.00e+00 pdb=" C7 NAG H 2 " 0.009 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.019 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.030 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.004 2.00e-02 2.50e+03 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 146 2.64 - 3.21: 15449 3.21 - 3.77: 25259 3.77 - 4.34: 36631 4.34 - 4.90: 61152 Nonbonded interactions: 138637 Sorted by model distance: nonbonded pdb=" NH2 ARG E 147 " pdb=" OE2 GLU E 208 " model vdw 2.076 3.120 nonbonded pdb=" OG SER A 82 " pdb=" O THR A 106 " model vdw 2.076 3.040 nonbonded pdb=" ND2 ASN B 305 " pdb=" OG SER B 457 " model vdw 2.108 3.120 nonbonded pdb=" OD2 ASP D 44 " pdb=" ND2 ASN D 47 " model vdw 2.138 3.120 nonbonded pdb=" OD2 ASP B 140 " pdb=" NE2 GLN B 142 " model vdw 2.151 3.120 ... (remaining 138632 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' selection = (chain 'D' and (resid 1 through 330 or resid 370 through 603)) } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.790 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 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 0.089 17523 Z= 0.308 Angle : 0.769 12.012 23935 Z= 0.344 Chirality : 0.049 0.517 2809 Planarity : 0.004 0.035 2885 Dihedral : 15.563 156.455 6916 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.19), residues: 2002 helix: 2.69 (0.18), residues: 764 sheet: -0.67 (0.25), residues: 401 loop : -0.58 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 147 TYR 0.015 0.001 TYR C 410 PHE 0.014 0.001 PHE A 225 TRP 0.010 0.001 TRP C 118 HIS 0.010 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00684 (17494) covalent geometry : angle 0.75588 (23855) SS BOND : bond 0.01056 ( 7) SS BOND : angle 2.32143 ( 14) hydrogen bonds : bond 0.13504 ( 850) hydrogen bonds : angle 6.31832 ( 2694) link_ALPHA1-6 : bond 0.00437 ( 6) link_ALPHA1-6 : angle 1.73978 ( 18) link_BETA1-4 : bond 0.00457 ( 9) link_BETA1-4 : angle 2.69079 ( 27) link_NAG-ASN : bond 0.03368 ( 7) link_NAG-ASN : angle 3.20870 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.726 Fit side-chains REVERT: A 97 ASP cc_start: 0.8039 (t70) cc_final: 0.7670 (t0) REVERT: E 332 TYR cc_start: 0.8347 (m-80) cc_final: 0.8027 (m-10) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.8226 time to fit residues: 84.9823 Evaluate side-chains 68 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS B 98 ASN B 276 GLN B 305 ASN C 39 ASN C 196 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.060657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.044849 restraints weight = 46427.818| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.37 r_work: 0.2510 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17523 Z= 0.166 Angle : 0.555 7.816 23935 Z= 0.278 Chirality : 0.045 0.334 2809 Planarity : 0.004 0.036 2885 Dihedral : 12.585 131.526 2993 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.59 % Allowed : 4.92 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.19), residues: 2002 helix: 3.07 (0.18), residues: 768 sheet: -0.31 (0.25), residues: 404 loop : -0.42 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 168 TYR 0.011 0.001 TYR B 439 PHE 0.021 0.001 PHE D 316 TRP 0.013 0.001 TRP D 60 HIS 0.006 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00381 (17494) covalent geometry : angle 0.54233 (23855) SS BOND : bond 0.00760 ( 7) SS BOND : angle 1.71169 ( 14) hydrogen bonds : bond 0.05163 ( 850) hydrogen bonds : angle 4.52958 ( 2694) link_ALPHA1-6 : bond 0.00674 ( 6) link_ALPHA1-6 : angle 1.94820 ( 18) link_BETA1-4 : bond 0.00578 ( 9) link_BETA1-4 : angle 2.25287 ( 27) link_NAG-ASN : bond 0.00150 ( 7) link_NAG-ASN : angle 2.38760 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.672 Fit side-chains REVERT: A 97 ASP cc_start: 0.8505 (t70) cc_final: 0.8089 (t0) REVERT: B 475 MET cc_start: 0.8087 (tpt) cc_final: 0.7800 (tpp) REVERT: D 407 ASP cc_start: 0.8387 (t0) cc_final: 0.8057 (t0) outliers start: 11 outliers final: 3 residues processed: 81 average time/residue: 0.7544 time to fit residues: 68.0374 Evaluate side-chains 73 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain D residue 222 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 152 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 153 optimal weight: 0.4980 chunk 140 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.059838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.044054 restraints weight = 47207.440| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 3.37 r_work: 0.2504 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17523 Z= 0.190 Angle : 0.522 7.924 23935 Z= 0.261 Chirality : 0.044 0.316 2809 Planarity : 0.003 0.032 2885 Dihedral : 11.043 109.703 2993 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.70 % Allowed : 6.95 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.19), residues: 2002 helix: 3.24 (0.18), residues: 764 sheet: -0.10 (0.25), residues: 388 loop : -0.45 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 168 TYR 0.011 0.001 TYR B 439 PHE 0.013 0.001 PHE D 280 TRP 0.012 0.001 TRP D 60 HIS 0.008 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00446 (17494) covalent geometry : angle 0.50887 (23855) SS BOND : bond 0.00709 ( 7) SS BOND : angle 1.62583 ( 14) hydrogen bonds : bond 0.04945 ( 850) hydrogen bonds : angle 4.24670 ( 2694) link_ALPHA1-6 : bond 0.00630 ( 6) link_ALPHA1-6 : angle 1.89644 ( 18) link_BETA1-4 : bond 0.00364 ( 9) link_BETA1-4 : angle 2.18425 ( 27) link_NAG-ASN : bond 0.00132 ( 7) link_NAG-ASN : angle 2.42784 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.564 Fit side-chains REVERT: A 97 ASP cc_start: 0.8520 (t70) cc_final: 0.8111 (t0) REVERT: D 117 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8722 (tpt) REVERT: D 310 GLN cc_start: 0.8912 (tp40) cc_final: 0.8597 (tp-100) REVERT: D 407 ASP cc_start: 0.8371 (t0) cc_final: 0.8020 (t0) outliers start: 13 outliers final: 6 residues processed: 79 average time/residue: 0.7202 time to fit residues: 63.4504 Evaluate side-chains 77 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 170 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.060916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.044938 restraints weight = 46652.733| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.45 r_work: 0.2516 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17523 Z= 0.138 Angle : 0.490 7.589 23935 Z= 0.245 Chirality : 0.043 0.300 2809 Planarity : 0.003 0.036 2885 Dihedral : 9.798 101.044 2993 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.02 % Allowed : 7.81 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.20), residues: 2002 helix: 3.39 (0.18), residues: 764 sheet: 0.05 (0.25), residues: 391 loop : -0.43 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 168 TYR 0.013 0.001 TYR D 190 PHE 0.013 0.001 PHE D 280 TRP 0.011 0.001 TRP A 311 HIS 0.004 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00316 (17494) covalent geometry : angle 0.47687 (23855) SS BOND : bond 0.00734 ( 7) SS BOND : angle 1.53488 ( 14) hydrogen bonds : bond 0.04524 ( 850) hydrogen bonds : angle 4.01677 ( 2694) link_ALPHA1-6 : bond 0.00788 ( 6) link_ALPHA1-6 : angle 1.85945 ( 18) link_BETA1-4 : bond 0.00380 ( 9) link_BETA1-4 : angle 1.92061 ( 27) link_NAG-ASN : bond 0.00096 ( 7) link_NAG-ASN : angle 2.34569 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.717 Fit side-chains REVERT: A 97 ASP cc_start: 0.8496 (t70) cc_final: 0.8093 (t0) REVERT: B 305 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8445 (t0) REVERT: C 436 ASP cc_start: 0.8452 (t0) cc_final: 0.8226 (t70) REVERT: D 241 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: D 407 ASP cc_start: 0.8402 (t0) cc_final: 0.8034 (t0) outliers start: 19 outliers final: 8 residues processed: 87 average time/residue: 0.6931 time to fit residues: 67.8492 Evaluate side-chains 80 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 144 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 96 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 191 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.060874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.045380 restraints weight = 46531.779| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 3.33 r_work: 0.2538 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17523 Z= 0.120 Angle : 0.474 7.076 23935 Z= 0.237 Chirality : 0.043 0.285 2809 Planarity : 0.003 0.040 2885 Dihedral : 9.055 98.574 2993 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.96 % Allowed : 8.56 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.20), residues: 2002 helix: 3.48 (0.18), residues: 765 sheet: 0.27 (0.26), residues: 393 loop : -0.39 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 168 TYR 0.010 0.001 TYR B 439 PHE 0.012 0.001 PHE D 280 TRP 0.011 0.001 TRP A 311 HIS 0.004 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00272 (17494) covalent geometry : angle 0.46259 (23855) SS BOND : bond 0.00733 ( 7) SS BOND : angle 1.46093 ( 14) hydrogen bonds : bond 0.04242 ( 850) hydrogen bonds : angle 3.86726 ( 2694) link_ALPHA1-6 : bond 0.00775 ( 6) link_ALPHA1-6 : angle 1.74489 ( 18) link_BETA1-4 : bond 0.00403 ( 9) link_BETA1-4 : angle 1.83542 ( 27) link_NAG-ASN : bond 0.00129 ( 7) link_NAG-ASN : angle 2.26265 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.756 Fit side-chains REVERT: A 97 ASP cc_start: 0.8462 (t70) cc_final: 0.8079 (t0) REVERT: B 305 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8382 (t0) REVERT: C 436 ASP cc_start: 0.8461 (t0) cc_final: 0.8198 (t70) REVERT: D 241 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: D 407 ASP cc_start: 0.8388 (t0) cc_final: 0.8017 (t0) outliers start: 18 outliers final: 8 residues processed: 84 average time/residue: 0.7302 time to fit residues: 68.3600 Evaluate side-chains 81 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.060707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.045068 restraints weight = 46519.451| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.34 r_work: 0.2526 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17523 Z= 0.144 Angle : 0.480 6.977 23935 Z= 0.240 Chirality : 0.043 0.283 2809 Planarity : 0.003 0.047 2885 Dihedral : 8.607 96.889 2993 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.86 % Allowed : 9.04 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.19), residues: 2002 helix: 3.48 (0.18), residues: 766 sheet: 0.29 (0.26), residues: 393 loop : -0.37 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 168 TYR 0.010 0.001 TYR B 439 PHE 0.012 0.001 PHE D 280 TRP 0.010 0.001 TRP A 311 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00335 (17494) covalent geometry : angle 0.46864 (23855) SS BOND : bond 0.00727 ( 7) SS BOND : angle 1.51423 ( 14) hydrogen bonds : bond 0.04263 ( 850) hydrogen bonds : angle 3.84822 ( 2694) link_ALPHA1-6 : bond 0.00752 ( 6) link_ALPHA1-6 : angle 1.74624 ( 18) link_BETA1-4 : bond 0.00363 ( 9) link_BETA1-4 : angle 1.85355 ( 27) link_NAG-ASN : bond 0.00163 ( 7) link_NAG-ASN : angle 2.21388 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.697 Fit side-chains REVERT: A 97 ASP cc_start: 0.8490 (t70) cc_final: 0.8148 (t0) REVERT: B 305 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8400 (t0) REVERT: C 436 ASP cc_start: 0.8475 (t0) cc_final: 0.8204 (t70) REVERT: D 241 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: D 404 MET cc_start: 0.8313 (ttm) cc_final: 0.8021 (ppp) REVERT: D 407 ASP cc_start: 0.8400 (t0) cc_final: 0.8017 (t0) outliers start: 16 outliers final: 9 residues processed: 84 average time/residue: 0.7334 time to fit residues: 68.8305 Evaluate side-chains 82 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 146 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN ** B 328 GLN ** 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 = 0.3100 r_free = 0.3100 target = 0.060969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.045319 restraints weight = 46713.328| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.35 r_work: 0.2531 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17523 Z= 0.132 Angle : 0.474 6.983 23935 Z= 0.237 Chirality : 0.042 0.282 2809 Planarity : 0.003 0.046 2885 Dihedral : 8.241 94.618 2993 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.02 % Allowed : 9.09 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.19), residues: 2002 helix: 3.50 (0.18), residues: 765 sheet: 0.32 (0.26), residues: 393 loop : -0.36 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 168 TYR 0.011 0.001 TYR B 439 PHE 0.012 0.001 PHE D 280 TRP 0.011 0.001 TRP A 311 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00305 (17494) covalent geometry : angle 0.46324 (23855) SS BOND : bond 0.00715 ( 7) SS BOND : angle 1.49113 ( 14) hydrogen bonds : bond 0.04175 ( 850) hydrogen bonds : angle 3.81562 ( 2694) link_ALPHA1-6 : bond 0.00767 ( 6) link_ALPHA1-6 : angle 1.68193 ( 18) link_BETA1-4 : bond 0.00393 ( 9) link_BETA1-4 : angle 1.75516 ( 27) link_NAG-ASN : bond 0.00164 ( 7) link_NAG-ASN : angle 2.19991 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.704 Fit side-chains REVERT: A 97 ASP cc_start: 0.8478 (t70) cc_final: 0.8113 (t0) REVERT: B 305 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8417 (t0) REVERT: C 436 ASP cc_start: 0.8386 (t0) cc_final: 0.8105 (t70) REVERT: D 241 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: D 407 ASP cc_start: 0.8410 (t0) cc_final: 0.8033 (t0) REVERT: E 448 ASP cc_start: 0.8056 (t0) cc_final: 0.7641 (t0) outliers start: 19 outliers final: 12 residues processed: 86 average time/residue: 0.7003 time to fit residues: 67.5726 Evaluate side-chains 85 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 0.0970 chunk 109 optimal weight: 0.0770 chunk 156 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN B 313 HIS ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS E 250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.062595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.046893 restraints weight = 46477.672| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.39 r_work: 0.2577 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17523 Z= 0.095 Angle : 0.461 10.515 23935 Z= 0.231 Chirality : 0.041 0.261 2809 Planarity : 0.003 0.052 2885 Dihedral : 7.745 90.583 2993 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.70 % Allowed : 9.68 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.20), residues: 2002 helix: 3.64 (0.18), residues: 765 sheet: 0.35 (0.26), residues: 395 loop : -0.29 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 168 TYR 0.010 0.001 TYR B 439 PHE 0.010 0.001 PHE D 280 TRP 0.012 0.001 TRP A 311 HIS 0.003 0.000 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00204 (17494) covalent geometry : angle 0.45106 (23855) SS BOND : bond 0.00707 ( 7) SS BOND : angle 1.56905 ( 14) hydrogen bonds : bond 0.03821 ( 850) hydrogen bonds : angle 3.66285 ( 2694) link_ALPHA1-6 : bond 0.00803 ( 6) link_ALPHA1-6 : angle 1.55494 ( 18) link_BETA1-4 : bond 0.00482 ( 9) link_BETA1-4 : angle 1.48075 ( 27) link_NAG-ASN : bond 0.00249 ( 7) link_NAG-ASN : angle 2.15156 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.686 Fit side-chains REVERT: B 58 MET cc_start: 0.8835 (ttm) cc_final: 0.8555 (ttp) REVERT: B 305 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8414 (t0) REVERT: C 436 ASP cc_start: 0.8389 (t0) cc_final: 0.8125 (t70) REVERT: D 241 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: D 407 ASP cc_start: 0.8376 (t0) cc_final: 0.7905 (t0) REVERT: E 448 ASP cc_start: 0.8038 (t0) cc_final: 0.7641 (t0) outliers start: 13 outliers final: 6 residues processed: 85 average time/residue: 0.7259 time to fit residues: 68.8329 Evaluate side-chains 78 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 16 optimal weight: 0.2980 chunk 65 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 22 optimal weight: 0.0470 chunk 107 optimal weight: 0.1980 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN ** B 328 GLN ** 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 = 0.3109 r_free = 0.3109 target = 0.061375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.045671 restraints weight = 46806.612| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.39 r_work: 0.2538 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17523 Z= 0.134 Angle : 0.475 7.017 23935 Z= 0.237 Chirality : 0.042 0.263 2809 Planarity : 0.003 0.062 2885 Dihedral : 7.625 89.877 2993 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.70 % Allowed : 9.73 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.20), residues: 2002 helix: 3.63 (0.18), residues: 765 sheet: 0.41 (0.26), residues: 393 loop : -0.29 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 168 TYR 0.010 0.001 TYR B 439 PHE 0.011 0.001 PHE D 280 TRP 0.010 0.001 TRP A 311 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00312 (17494) covalent geometry : angle 0.46476 (23855) SS BOND : bond 0.00721 ( 7) SS BOND : angle 1.68183 ( 14) hydrogen bonds : bond 0.03971 ( 850) hydrogen bonds : angle 3.72634 ( 2694) link_ALPHA1-6 : bond 0.00729 ( 6) link_ALPHA1-6 : angle 1.63034 ( 18) link_BETA1-4 : bond 0.00357 ( 9) link_BETA1-4 : angle 1.67064 ( 27) link_NAG-ASN : bond 0.00165 ( 7) link_NAG-ASN : angle 2.08756 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.706 Fit side-chains REVERT: B 58 MET cc_start: 0.8833 (ttm) cc_final: 0.8535 (ttp) REVERT: B 305 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8384 (t0) REVERT: C 436 ASP cc_start: 0.8365 (t0) cc_final: 0.8101 (t70) REVERT: D 241 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: D 407 ASP cc_start: 0.8396 (t0) cc_final: 0.7914 (t0) REVERT: E 448 ASP cc_start: 0.8045 (t0) cc_final: 0.7654 (t0) outliers start: 13 outliers final: 9 residues processed: 82 average time/residue: 0.7387 time to fit residues: 67.5922 Evaluate side-chains 82 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 328 PHE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 37 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 124 optimal weight: 0.0270 chunk 21 optimal weight: 0.9990 overall best weight: 1.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.061675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.045984 restraints weight = 46379.141| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.38 r_work: 0.2550 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17523 Z= 0.119 Angle : 0.478 11.978 23935 Z= 0.237 Chirality : 0.042 0.261 2809 Planarity : 0.003 0.063 2885 Dihedral : 7.499 88.499 2993 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.70 % Allowed : 9.68 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.20), residues: 2002 helix: 3.64 (0.18), residues: 766 sheet: 0.39 (0.26), residues: 395 loop : -0.27 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 168 TYR 0.010 0.001 TYR B 439 PHE 0.011 0.001 PHE D 280 TRP 0.010 0.001 TRP A 311 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00274 (17494) covalent geometry : angle 0.46808 (23855) SS BOND : bond 0.00714 ( 7) SS BOND : angle 1.60580 ( 14) hydrogen bonds : bond 0.03924 ( 850) hydrogen bonds : angle 3.70211 ( 2694) link_ALPHA1-6 : bond 0.00734 ( 6) link_ALPHA1-6 : angle 1.55507 ( 18) link_BETA1-4 : bond 0.00399 ( 9) link_BETA1-4 : angle 1.60068 ( 27) link_NAG-ASN : bond 0.00168 ( 7) link_NAG-ASN : angle 2.09686 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.714 Fit side-chains REVERT: B 58 MET cc_start: 0.8846 (ttm) cc_final: 0.8557 (ttp) REVERT: B 305 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8357 (t0) REVERT: C 436 ASP cc_start: 0.8366 (t0) cc_final: 0.8102 (t70) REVERT: D 241 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: D 407 ASP cc_start: 0.8373 (t0) cc_final: 0.7881 (t0) REVERT: E 448 ASP cc_start: 0.8047 (t0) cc_final: 0.7659 (t0) outliers start: 13 outliers final: 7 residues processed: 82 average time/residue: 0.7314 time to fit residues: 67.0676 Evaluate side-chains 80 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 129 optimal weight: 0.0970 chunk 69 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.061880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.046186 restraints weight = 46830.021| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.42 r_work: 0.2549 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17523 Z= 0.113 Angle : 0.471 8.330 23935 Z= 0.235 Chirality : 0.042 0.259 2809 Planarity : 0.003 0.061 2885 Dihedral : 7.279 86.055 2993 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.53 % Allowed : 9.79 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.20), residues: 2002 helix: 3.63 (0.18), residues: 766 sheet: 0.41 (0.26), residues: 397 loop : -0.26 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 168 TYR 0.010 0.001 TYR B 439 PHE 0.018 0.001 PHE E 328 TRP 0.010 0.001 TRP A 311 HIS 0.003 0.000 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00259 (17494) covalent geometry : angle 0.46110 (23855) SS BOND : bond 0.00712 ( 7) SS BOND : angle 1.56870 ( 14) hydrogen bonds : bond 0.03871 ( 850) hydrogen bonds : angle 3.68438 ( 2694) link_ALPHA1-6 : bond 0.00726 ( 6) link_ALPHA1-6 : angle 1.53721 ( 18) link_BETA1-4 : bond 0.00408 ( 9) link_BETA1-4 : angle 1.59080 ( 27) link_NAG-ASN : bond 0.00176 ( 7) link_NAG-ASN : angle 2.06979 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4514.44 seconds wall clock time: 78 minutes 20.40 seconds (4700.40 seconds total)