Starting phenix.real_space_refine on Sun Jun 15 22:45:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6y_28892/06_2025/8f6y_28892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6y_28892/06_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_28892/06_2025/8f6y_28892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6y_28892/06_2025/8f6y_28892.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6y_28892/06_2025/8f6y_28892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6y_28892/06_2025/8f6y_28892.cif" } resolution = 2.79 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= 0.002 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.91, per 1000 atoms: 0.64 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: 5.14 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.01 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: 5.66 Time building geometry restraints manager: 5.91 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 426 or resid 601 throug \ h 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: 1.470 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: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 41.620 Find NCS groups from input model: 0.630 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: 0.010 Load rotamer database and sin/cos tables:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.640 ------------------------------------------------------------------------------- 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 (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: 0.98 (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 TRP 0.010 0.001 TRP C 118 HIS 0.010 0.001 HIS B 103 PHE 0.014 0.001 PHE A 225 TYR 0.015 0.001 TYR C 410 ARG 0.006 0.001 ARG E 147 Details of bonding type rmsd link_NAG-ASN : bond 0.03368 ( 7) link_NAG-ASN : angle 3.20870 ( 21) 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) hydrogen bonds : bond 0.13504 ( 850) hydrogen bonds : angle 6.31832 ( 2694) SS BOND : bond 0.01056 ( 7) SS BOND : angle 2.32143 ( 14) covalent geometry : bond 0.00684 (17494) covalent geometry : angle 0.75588 (23855) *********************** 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 : 1.913 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: 1.6521 time to fit residues: 171.5223 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 : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3103 r_free = 0.3103 target = 0.061264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.045445 restraints weight = 46131.489| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.37 r_work: 0.2532 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17523 Z= 0.135 Angle : 0.544 7.570 23935 Z= 0.272 Chirality : 0.044 0.327 2809 Planarity : 0.004 0.037 2885 Dihedral : 12.508 129.972 2993 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.64 % Allowed : 4.65 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 1.48 (0.19), residues: 2002 helix: 3.10 (0.18), residues: 769 sheet: -0.29 (0.25), residues: 404 loop : -0.39 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 118 HIS 0.005 0.001 HIS B 103 PHE 0.022 0.001 PHE D 316 TYR 0.011 0.001 TYR B 439 ARG 0.008 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 7) link_NAG-ASN : angle 2.33432 ( 21) link_ALPHA1-6 : bond 0.00688 ( 6) link_ALPHA1-6 : angle 1.92303 ( 18) link_BETA1-4 : bond 0.00651 ( 9) link_BETA1-4 : angle 2.19537 ( 27) hydrogen bonds : bond 0.05065 ( 850) hydrogen bonds : angle 4.49878 ( 2694) SS BOND : bond 0.00757 ( 7) SS BOND : angle 1.64423 ( 14) covalent geometry : bond 0.00300 (17494) covalent geometry : angle 0.53091 (23855) *********************** 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 86 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 1.869 Fit side-chains REVERT: A 97 ASP cc_start: 0.8487 (t70) cc_final: 0.8089 (t0) REVERT: D 407 ASP cc_start: 0.8381 (t0) cc_final: 0.8048 (t0) outliers start: 12 outliers final: 3 residues processed: 81 average time/residue: 1.4639 time to fit residues: 132.5328 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 : 1.841 ------------------------------------------------------------------------------- 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 80 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3101 r_free = 0.3101 target = 0.061018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.045250 restraints weight = 46337.922| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 3.35 r_work: 0.2538 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17523 Z= 0.138 Angle : 0.493 7.356 23935 Z= 0.247 Chirality : 0.043 0.297 2809 Planarity : 0.003 0.034 2885 Dihedral : 10.888 106.763 2993 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.70 % Allowed : 6.52 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 1.70 (0.19), residues: 2002 helix: 3.33 (0.18), residues: 766 sheet: 0.01 (0.25), residues: 393 loop : -0.41 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 60 HIS 0.006 0.001 HIS B 103 PHE 0.013 0.001 PHE D 280 TYR 0.010 0.001 TYR B 439 ARG 0.009 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 7) link_NAG-ASN : angle 2.28780 ( 21) link_ALPHA1-6 : bond 0.00677 ( 6) link_ALPHA1-6 : angle 1.81796 ( 18) link_BETA1-4 : bond 0.00394 ( 9) link_BETA1-4 : angle 2.05958 ( 27) hydrogen bonds : bond 0.04663 ( 850) hydrogen bonds : angle 4.11950 ( 2694) SS BOND : bond 0.00746 ( 7) SS BOND : angle 1.50099 ( 14) covalent geometry : bond 0.00316 (17494) covalent geometry : angle 0.48074 (23855) *********************** 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 87 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.962 Fit side-chains REVERT: A 97 ASP cc_start: 0.8486 (t70) cc_final: 0.8180 (t0) REVERT: D 117 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8723 (tpt) REVERT: D 407 ASP cc_start: 0.8374 (t0) cc_final: 0.8041 (t0) outliers start: 13 outliers final: 5 residues processed: 80 average time/residue: 1.4750 time to fit residues: 132.9979 Evaluate side-chains 75 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 111 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 174 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 142 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.062967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.047201 restraints weight = 46056.722| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.38 r_work: 0.2572 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17523 Z= 0.097 Angle : 0.467 6.605 23935 Z= 0.235 Chirality : 0.042 0.270 2809 Planarity : 0.003 0.034 2885 Dihedral : 9.367 96.447 2993 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.07 % Allowed : 6.84 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 1.93 (0.20), residues: 2002 helix: 3.46 (0.18), residues: 773 sheet: 0.20 (0.25), residues: 414 loop : -0.30 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 187 HIS 0.004 0.000 HIS D 204 PHE 0.013 0.001 PHE D 316 TYR 0.014 0.001 TYR D 190 ARG 0.006 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 7) link_NAG-ASN : angle 2.08735 ( 21) link_ALPHA1-6 : bond 0.00875 ( 6) link_ALPHA1-6 : angle 1.72462 ( 18) link_BETA1-4 : bond 0.00512 ( 9) link_BETA1-4 : angle 1.68779 ( 27) hydrogen bonds : bond 0.04056 ( 850) hydrogen bonds : angle 3.83216 ( 2694) SS BOND : bond 0.00739 ( 7) SS BOND : angle 1.35185 ( 14) covalent geometry : bond 0.00202 (17494) covalent geometry : angle 0.45674 (23855) *********************** 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 96 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 1.872 Fit side-chains REVERT: A 97 ASP cc_start: 0.8463 (t70) cc_final: 0.8193 (t0) REVERT: C 436 ASP cc_start: 0.8487 (t0) cc_final: 0.8257 (t70) REVERT: D 407 ASP cc_start: 0.8350 (t0) cc_final: 0.7923 (t0) outliers start: 20 outliers final: 7 residues processed: 89 average time/residue: 1.4401 time to fit residues: 143.5700 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 : 1.885 ------------------------------------------------------------------------------- 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 317 ILE 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 82 optimal weight: 3.9990 chunk 142 optimal weight: 0.0770 chunk 116 optimal weight: 2.9990 chunk 150 optimal weight: 0.0010 chunk 17 optimal weight: 0.0070 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 overall best weight: 0.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN B 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.063053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.047503 restraints weight = 46413.324| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.38 r_work: 0.2597 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17523 Z= 0.094 Angle : 0.452 6.539 23935 Z= 0.227 Chirality : 0.042 0.248 2809 Planarity : 0.003 0.043 2885 Dihedral : 8.655 94.699 2993 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.70 % Allowed : 8.07 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 2.03 (0.19), residues: 2002 helix: 3.51 (0.18), residues: 773 sheet: 0.36 (0.25), residues: 408 loop : -0.26 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.005 0.001 HIS D 408 PHE 0.012 0.001 PHE D 280 TYR 0.008 0.001 TYR B 439 ARG 0.007 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 7) link_NAG-ASN : angle 1.97184 ( 21) link_ALPHA1-6 : bond 0.00783 ( 6) link_ALPHA1-6 : angle 1.65229 ( 18) link_BETA1-4 : bond 0.00469 ( 9) link_BETA1-4 : angle 1.72665 ( 27) hydrogen bonds : bond 0.03836 ( 850) hydrogen bonds : angle 3.67334 ( 2694) SS BOND : bond 0.00724 ( 7) SS BOND : angle 1.34507 ( 14) covalent geometry : bond 0.00200 (17494) covalent geometry : angle 0.44130 (23855) *********************** 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 87 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 2.079 Fit side-chains REVERT: C 436 ASP cc_start: 0.8482 (t0) cc_final: 0.8238 (t70) REVERT: D 407 ASP cc_start: 0.8306 (t0) cc_final: 0.7851 (t0) REVERT: E 448 ASP cc_start: 0.7986 (t0) cc_final: 0.7554 (t0) outliers start: 13 outliers final: 5 residues processed: 83 average time/residue: 1.4712 time to fit residues: 137.1208 Evaluate side-chains 74 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain D residue 317 ILE 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 101 optimal weight: 0.4980 chunk 146 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 15 optimal weight: 0.2980 chunk 108 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN E 250 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.063675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.047958 restraints weight = 46382.266| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.39 r_work: 0.2598 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17523 Z= 0.095 Angle : 0.455 9.128 23935 Z= 0.227 Chirality : 0.042 0.244 2809 Planarity : 0.003 0.046 2885 Dihedral : 8.208 92.062 2993 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.59 % Allowed : 8.34 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 2.11 (0.20), residues: 2002 helix: 3.59 (0.18), residues: 771 sheet: 0.44 (0.26), residues: 406 loop : -0.26 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.003 0.000 HIS D 204 PHE 0.011 0.001 PHE D 280 TYR 0.009 0.001 TYR B 439 ARG 0.010 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 7) link_NAG-ASN : angle 1.87074 ( 21) link_ALPHA1-6 : bond 0.00815 ( 6) link_ALPHA1-6 : angle 1.59721 ( 18) link_BETA1-4 : bond 0.00483 ( 9) link_BETA1-4 : angle 1.57644 ( 27) hydrogen bonds : bond 0.03723 ( 850) hydrogen bonds : angle 3.63309 ( 2694) SS BOND : bond 0.00701 ( 7) SS BOND : angle 1.33908 ( 14) covalent geometry : bond 0.00207 (17494) covalent geometry : angle 0.44614 (23855) *********************** 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 86 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 1.903 Fit side-chains REVERT: C 436 ASP cc_start: 0.8429 (t0) cc_final: 0.8200 (t70) REVERT: D 407 ASP cc_start: 0.8279 (t0) cc_final: 0.7826 (t0) REVERT: E 448 ASP cc_start: 0.7977 (t0) cc_final: 0.7571 (t0) outliers start: 11 outliers final: 5 residues processed: 81 average time/residue: 1.4304 time to fit residues: 130.0311 Evaluate side-chains 76 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain D residue 317 ILE 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 7 optimal weight: 0.1980 chunk 2 optimal weight: 7.9990 chunk 182 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 184 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 0.0020 chunk 60 optimal weight: 4.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN C 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.063698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.048254 restraints weight = 46086.586| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.32 r_work: 0.2619 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2264 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= 0.091 Angle : 0.450 7.574 23935 Z= 0.224 Chirality : 0.041 0.235 2809 Planarity : 0.003 0.049 2885 Dihedral : 7.756 87.269 2993 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.43 % Allowed : 8.93 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 2.18 (0.20), residues: 2002 helix: 3.63 (0.18), residues: 772 sheet: 0.51 (0.26), residues: 408 loop : -0.23 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.003 0.000 HIS D 204 PHE 0.011 0.001 PHE D 280 TYR 0.008 0.001 TYR B 439 ARG 0.014 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 7) link_NAG-ASN : angle 1.82077 ( 21) link_ALPHA1-6 : bond 0.00788 ( 6) link_ALPHA1-6 : angle 1.53061 ( 18) link_BETA1-4 : bond 0.00498 ( 9) link_BETA1-4 : angle 1.51040 ( 27) hydrogen bonds : bond 0.03567 ( 850) hydrogen bonds : angle 3.54942 ( 2694) SS BOND : bond 0.00698 ( 7) SS BOND : angle 1.31437 ( 14) covalent geometry : bond 0.00198 (17494) covalent geometry : angle 0.44133 (23855) *********************** 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 83 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 1.987 Fit side-chains REVERT: D 407 ASP cc_start: 0.8285 (t0) cc_final: 0.7835 (t0) REVERT: E 328 PHE cc_start: 0.6529 (t80) cc_final: 0.6328 (t80) REVERT: E 448 ASP cc_start: 0.7951 (t0) cc_final: 0.7547 (t0) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 1.4693 time to fit residues: 131.6482 Evaluate side-chains 77 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain D residue 317 ILE 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 157 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 182 optimal weight: 0.3980 chunk 192 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 177 optimal weight: 0.0770 overall best weight: 1.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.046055 restraints weight = 46841.570| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.34 r_work: 0.2556 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2114 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= 0.146 Angle : 0.489 11.686 23935 Z= 0.241 Chirality : 0.042 0.243 2809 Planarity : 0.003 0.057 2885 Dihedral : 7.624 87.227 2993 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.48 % Allowed : 9.36 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 2.16 (0.20), residues: 2002 helix: 3.61 (0.18), residues: 768 sheet: 0.55 (0.26), residues: 393 loop : -0.23 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 311 HIS 0.005 0.001 HIS B 60 PHE 0.012 0.001 PHE D 280 TYR 0.010 0.001 TYR B 439 ARG 0.011 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 7) link_NAG-ASN : angle 1.83307 ( 21) link_ALPHA1-6 : bond 0.00701 ( 6) link_ALPHA1-6 : angle 1.61650 ( 18) link_BETA1-4 : bond 0.00363 ( 9) link_BETA1-4 : angle 1.73188 ( 27) hydrogen bonds : bond 0.03912 ( 850) hydrogen bonds : angle 3.69171 ( 2694) SS BOND : bond 0.00698 ( 7) SS BOND : angle 1.49729 ( 14) covalent geometry : bond 0.00337 (17494) covalent geometry : angle 0.48017 (23855) *********************** 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 80 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.965 Fit side-chains REVERT: A 178 MET cc_start: 0.9565 (mmm) cc_final: 0.9316 (tpp) REVERT: D 324 MET cc_start: 0.6605 (mmt) cc_final: 0.6284 (mtp) REVERT: D 407 ASP cc_start: 0.8309 (t0) cc_final: 0.7857 (t0) REVERT: E 328 PHE cc_start: 0.6589 (t80) cc_final: 0.6379 (OUTLIER) REVERT: E 448 ASP cc_start: 0.8011 (t0) cc_final: 0.7603 (t0) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 1.4998 time to fit residues: 128.9684 Evaluate side-chains 74 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 125 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 145 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 121 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN D 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.062947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.047292 restraints weight = 46575.267| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.40 r_work: 0.2585 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17523 Z= 0.101 Angle : 0.459 7.597 23935 Z= 0.230 Chirality : 0.041 0.241 2809 Planarity : 0.003 0.057 2885 Dihedral : 7.292 84.051 2993 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.37 % Allowed : 9.52 % 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 (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: 2.19 (0.20), residues: 2002 helix: 3.66 (0.18), residues: 767 sheet: 0.51 (0.26), residues: 406 loop : -0.20 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.003 0.000 HIS D 204 PHE 0.010 0.001 PHE D 280 TYR 0.010 0.001 TYR B 439 ARG 0.013 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 7) link_NAG-ASN : angle 1.86589 ( 21) link_ALPHA1-6 : bond 0.00754 ( 6) link_ALPHA1-6 : angle 1.48837 ( 18) link_BETA1-4 : bond 0.00477 ( 9) link_BETA1-4 : angle 1.54595 ( 27) hydrogen bonds : bond 0.03702 ( 850) hydrogen bonds : angle 3.61346 ( 2694) SS BOND : bond 0.00687 ( 7) SS BOND : angle 1.38803 ( 14) covalent geometry : bond 0.00226 (17494) covalent geometry : angle 0.45065 (23855) *********************** 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 79 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 2.017 Fit side-chains REVERT: D 407 ASP cc_start: 0.8311 (t0) cc_final: 0.7843 (t0) REVERT: E 328 PHE cc_start: 0.6474 (t80) cc_final: 0.6262 (OUTLIER) REVERT: E 448 ASP cc_start: 0.7979 (t0) cc_final: 0.7573 (t0) outliers start: 7 outliers final: 7 residues processed: 75 average time/residue: 1.5522 time to fit residues: 129.7503 Evaluate side-chains 75 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain D residue 317 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.060171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.044705 restraints weight = 47045.930| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.33 r_work: 0.2523 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17523 Z= 0.198 Angle : 0.530 11.527 23935 Z= 0.262 Chirality : 0.043 0.261 2809 Planarity : 0.003 0.067 2885 Dihedral : 7.380 85.157 2993 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.27 % Allowed : 9.84 % 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 (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: 2.07 (0.20), residues: 2002 helix: 3.54 (0.18), residues: 767 sheet: 0.47 (0.26), residues: 392 loop : -0.26 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 118 HIS 0.007 0.001 HIS B 103 PHE 0.012 0.001 PHE D 280 TYR 0.011 0.001 TYR B 439 ARG 0.014 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 7) link_NAG-ASN : angle 1.94488 ( 21) link_ALPHA1-6 : bond 0.00655 ( 6) link_ALPHA1-6 : angle 1.68180 ( 18) link_BETA1-4 : bond 0.00314 ( 9) link_BETA1-4 : angle 1.94804 ( 27) hydrogen bonds : bond 0.04278 ( 850) hydrogen bonds : angle 3.85538 ( 2694) SS BOND : bond 0.00709 ( 7) SS BOND : angle 1.65675 ( 14) covalent geometry : bond 0.00462 (17494) covalent geometry : angle 0.52022 (23855) ********************** 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 75 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 2.013 Fit side-chains REVERT: D 407 ASP cc_start: 0.8385 (t0) cc_final: 0.7948 (t0) REVERT: E 328 PHE cc_start: 0.6535 (t80) cc_final: 0.6331 (OUTLIER) REVERT: E 448 ASP cc_start: 0.8012 (t0) cc_final: 0.7605 (t0) outliers start: 5 outliers final: 6 residues processed: 72 average time/residue: 1.5771 time to fit residues: 126.3350 Evaluate side-chains 73 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 124 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 107 optimal weight: 0.2980 chunk 128 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 139 optimal weight: 8.9990 chunk 46 optimal weight: 0.0980 chunk 96 optimal weight: 10.0000 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN C 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.062512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.046824 restraints weight = 46455.264| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.40 r_work: 0.2569 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17523 Z= 0.100 Angle : 0.466 7.639 23935 Z= 0.234 Chirality : 0.042 0.250 2809 Planarity : 0.003 0.058 2885 Dihedral : 7.118 83.835 2993 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.32 % Allowed : 9.89 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: 2.16 (0.20), residues: 2002 helix: 3.65 (0.18), residues: 766 sheet: 0.53 (0.26), residues: 395 loop : -0.25 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 60 HIS 0.003 0.000 HIS D 385 PHE 0.010 0.001 PHE D 280 TYR 0.010 0.001 TYR B 439 ARG 0.015 0.000 ARG C 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 7) link_NAG-ASN : angle 1.93522 ( 21) link_ALPHA1-6 : bond 0.00772 ( 6) link_ALPHA1-6 : angle 1.50216 ( 18) link_BETA1-4 : bond 0.00470 ( 9) link_BETA1-4 : angle 1.54673 ( 27) hydrogen bonds : bond 0.03820 ( 850) hydrogen bonds : angle 3.66411 ( 2694) SS BOND : bond 0.00690 ( 7) SS BOND : angle 1.42382 ( 14) covalent geometry : bond 0.00219 (17494) covalent geometry : angle 0.45735 (23855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8641.24 seconds wall clock time: 149 minutes 9.47 seconds (8949.47 seconds total)