Starting phenix.real_space_refine on Thu Sep 18 04:50:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fez_50346/09_2025/9fez_50346.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fez_50346/09_2025/9fez_50346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fez_50346/09_2025/9fez_50346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fez_50346/09_2025/9fez_50346.map" model { file = "/net/cci-nas-00/data/ceres_data/9fez_50346/09_2025/9fez_50346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fez_50346/09_2025/9fez_50346.cif" } resolution = 3.3 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 9295 2.51 5 N 2270 2.21 5 O 2605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14250 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2739 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Conformer: "B" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} bond proxies already assigned to first conformer: 2793 Chain: "B" Number of atoms: 2739 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Conformer: "B" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} bond proxies already assigned to first conformer: 2793 Chain: "C" Number of atoms: 2739 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Conformer: "B" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} bond proxies already assigned to first conformer: 2793 Chain: "D" Number of atoms: 2739 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Conformer: "B" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} bond proxies already assigned to first conformer: 2793 Chain: "E" Number of atoms: 2739 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Conformer: "B" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} bond proxies already assigned to first conformer: 2793 Chain: "a" 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" 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: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 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: "d" 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: "I" 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: "e" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.06, per 1000 atoms: 0.43 Number of scatterers: 14250 At special positions: 0 Unit cell: (100.434, 100.434, 130.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2605 8.00 N 2270 7.00 C 9295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A 501 " - " ASN A 8 " " NAG B 502 " - " ASN B 8 " " NAG C 502 " - " ASN C 8 " " NAG D 502 " - " ASN D 8 " " NAG E 502 " - " ASN E 8 " " NAG F 1 " - " ASN A 80 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN C 80 " " NAG I 1 " - " ASN D 80 " " NAG J 1 " - " ASN E 80 " " NAG a 1 " - " ASN A 149 " " NAG b 1 " - " ASN B 149 " " NAG c 1 " - " ASN C 149 " " NAG d 1 " - " ASN D 149 " " NAG e 1 " - " ASN E 149 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 891.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 43.0% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 139 through 143 removed outlier: 4.306A pdb=" N ARG A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 237 removed outlier: 3.770A pdb=" N SER A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 246 through 272 Processing helix chain 'A' and resid 279 through 306 Processing helix chain 'A' and resid 309 through 446 Proline residue: A 432 - end of helix Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.690A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.378A pdb=" N ARG B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 246 through 271 Processing helix chain 'B' and resid 279 through 306 Processing helix chain 'B' and resid 309 through 447 removed outlier: 3.916A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 239 removed outlier: 3.911A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 271 Processing helix chain 'C' and resid 279 through 307 removed outlier: 4.591A pdb=" N PHE C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 447 Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 9 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.597A pdb=" N LEU D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 4.457A pdb=" N ARG D 142 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 239 removed outlier: 3.971A pdb=" N SER D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 279 through 307 removed outlier: 4.451A pdb=" N PHE D 307 " --> pdb=" O ASN D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 446 removed outlier: 3.605A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.719A pdb=" N LEU E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 226 removed outlier: 3.723A pdb=" N TYR E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 239 Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 246 through 272 removed outlier: 3.596A pdb=" N ARG E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 306 removed outlier: 3.726A pdb=" N MET E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 447 removed outlier: 3.839A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 46 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 36 through 46 current: chain 'A' and resid 56 through 68 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 68 current: chain 'A' and resid 123 through 135 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 4.014A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 51 removed outlier: 6.746A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 68 current: chain 'B' and resid 123 through 135 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.029A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL B 199 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B 205 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN B 197 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG B 207 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER B 195 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER B 209 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU B 193 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER B 211 " --> pdb=" O HIS B 191 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS B 191 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG B 213 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 51 removed outlier: 6.538A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C 43 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 68 current: chain 'C' and resid 123 through 135 Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 98 removed outlier: 4.125A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 36 through 51 removed outlier: 9.965A pdb=" N GLY D 39 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ARG D 68 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ASN D 41 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR D 66 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ASP D 43 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLN D 64 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA D 45 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N TYR D 62 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE D 47 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR D 60 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 56 through 68 current: chain 'D' and resid 123 through 135 Processing sheet with id=AA8, first strand: chain 'D' and resid 96 through 98 removed outlier: 4.000A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 36 through 51 removed outlier: 9.871A pdb=" N GLY E 39 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ARG E 68 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASN E 41 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TYR E 66 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASP E 43 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLN E 64 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA E 45 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N TYR E 62 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE E 47 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR E 60 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET E 49 " --> pdb=" O THR E 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 68 current: chain 'E' and resid 123 through 135 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.134A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR E 205 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN E 197 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG E 207 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER E 195 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER E 209 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU E 193 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER E 211 " --> pdb=" O HIS E 191 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS E 191 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG E 213 " --> pdb=" O VAL E 189 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1678 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: 2.23 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4267 1.34 - 1.46: 3177 1.46 - 1.57: 7046 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14630 Sorted by residual: bond pdb=" C1 MAN e 5 " pdb=" O5 MAN e 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 MAN e 4 " pdb=" O5 MAN e 4 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 MAN b 5 " pdb=" O5 MAN b 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 MAN a 5 " pdb=" O5 MAN a 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C1 MAN d 5 " pdb=" O5 MAN d 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.40e+00 ... (remaining 14625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 18993 1.12 - 2.24: 655 2.24 - 3.36: 222 3.36 - 4.49: 29 4.49 - 5.61: 16 Bond angle restraints: 19915 Sorted by residual: angle pdb=" N ILE E 429 " pdb=" CA ILE E 429 " pdb=" C ILE E 429 " ideal model delta sigma weight residual 112.96 109.44 3.52 1.00e+00 1.00e+00 1.24e+01 angle pdb=" CA TYR E 299 " pdb=" CB TYR E 299 " pdb=" CG TYR E 299 " ideal model delta sigma weight residual 113.90 108.54 5.36 1.80e+00 3.09e-01 8.86e+00 angle pdb=" C ILE B 218 " pdb=" CA ILE B 218 " pdb=" CB ILE B 218 " ideal model delta sigma weight residual 111.20 107.99 3.21 1.24e+00 6.50e-01 6.69e+00 angle pdb=" C GLY C 219 " pdb=" N TYR C 220 " pdb=" CA TYR C 220 " ideal model delta sigma weight residual 120.38 123.97 -3.59 1.46e+00 4.69e-01 6.05e+00 angle pdb=" C ILE E 218 " pdb=" CA ILE E 218 " pdb=" CB ILE E 218 " ideal model delta sigma weight residual 111.20 108.22 2.98 1.24e+00 6.50e-01 5.77e+00 ... (remaining 19910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 8773 21.17 - 42.34: 223 42.34 - 63.51: 28 63.51 - 84.67: 41 84.67 - 105.84: 20 Dihedral angle restraints: 9085 sinusoidal: 4120 harmonic: 4965 Sorted by residual: dihedral pdb=" O4 BMA e 3 " pdb=" C4 BMA e 3 " pdb=" C5 BMA e 3 " pdb=" O5 BMA e 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.13 105.84 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" O4 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C5 BMA b 3 " pdb=" O5 BMA b 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.92 105.63 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA c 3 " pdb=" C4 BMA c 3 " pdb=" C5 BMA c 3 " pdb=" O5 BMA c 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.42 105.13 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 9082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1908 0.052 - 0.103: 354 0.103 - 0.155: 68 0.155 - 0.206: 9 0.206 - 0.258: 11 Chirality restraints: 2350 Sorted by residual: chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C5 BMA c 3 " pdb=" C4 BMA c 3 " pdb=" C6 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C5 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C6 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2347 not shown) Planarity restraints: 2425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 299 " 0.017 2.00e-02 2.50e+03 1.06e-02 2.24e+00 pdb=" CG TYR E 299 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR E 299 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR E 299 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 299 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 299 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 299 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 299 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 275 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO E 276 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 143 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 144 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 144 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 144 " -0.016 5.00e-02 4.00e+02 ... (remaining 2422 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3463 2.80 - 3.32: 13239 3.32 - 3.85: 24402 3.85 - 4.37: 28482 4.37 - 4.90: 48789 Nonbonded interactions: 118375 Sorted by model distance: nonbonded pdb=" OG1 THR A 202 " pdb=" OH TYR A 205 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR A 284 " pdb=" OD1 ASN A 439 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASN A 8 " pdb=" OG SER A 10 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR E 284 " pdb=" OD1 ASN E 439 " model vdw 2.285 3.040 nonbonded pdb=" OD2 ASP A 146 " pdb=" NE2 GLN A 148 " model vdw 2.291 3.120 ... (remaining 118370 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 65 or resid 67 through 447)) selection = (chain 'B' and (resid 8 through 65 or resid 67 through 447)) selection = (chain 'C' and (resid 8 through 65 or resid 67 through 447)) selection = (chain 'D' and (resid 8 through 65 or resid 67 through 447)) selection = (chain 'E' and (resid 8 through 65 or resid 67 through 447)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.600 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.080 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14675 Z= 0.182 Angle : 0.567 5.607 20045 Z= 0.277 Chirality : 0.045 0.258 2350 Planarity : 0.003 0.032 2410 Dihedral : 12.551 105.843 5890 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.07 % Allowed : 3.01 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.88 (0.22), residues: 1660 helix: 2.62 (0.21), residues: 616 sheet: 0.58 (0.26), residues: 411 loop : 0.43 (0.29), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 86 TYR 0.024 0.001 TYR E 299 PHE 0.010 0.001 PHE A 63 TRP 0.010 0.001 TRP E 67 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00382 (14630) covalent geometry : angle 0.55925 (19915) SS BOND : bond 0.00180 ( 5) SS BOND : angle 0.38711 ( 10) hydrogen bonds : bond 0.10657 ( 602) hydrogen bonds : angle 4.70175 ( 1678) link_ALPHA1-3 : bond 0.00399 ( 5) link_ALPHA1-3 : angle 1.13190 ( 15) link_ALPHA1-6 : bond 0.00371 ( 5) link_ALPHA1-6 : angle 1.13254 ( 15) link_BETA1-4 : bond 0.00370 ( 15) link_BETA1-4 : angle 1.51450 ( 45) link_NAG-ASN : bond 0.00156 ( 15) link_NAG-ASN : angle 1.23859 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 457 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8813 (mtp) cc_final: 0.8442 (ttm) REVERT: A 153 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8304 (mm-30) REVERT: A 163 ASP cc_start: 0.8289 (m-30) cc_final: 0.7970 (m-30) REVERT: A 180 ARG cc_start: 0.8530 (mtm110) cc_final: 0.8016 (mtp-110) REVERT: A 200 PHE cc_start: 0.8504 (m-80) cc_final: 0.8231 (m-80) REVERT: A 297 LEU cc_start: 0.9232 (tp) cc_final: 0.8999 (tt) REVERT: B 95 ASP cc_start: 0.8484 (p0) cc_final: 0.8277 (p0) REVERT: B 172 ASP cc_start: 0.8075 (m-30) cc_final: 0.7786 (t0) REVERT: B 247 SER cc_start: 0.9022 (p) cc_final: 0.8613 (t) REVERT: B 309 GLN cc_start: 0.8040 (mt0) cc_final: 0.7543 (mp-120) REVERT: B 426 TRP cc_start: 0.8049 (m100) cc_final: 0.7482 (m100) REVERT: C 13 LYS cc_start: 0.9110 (tttt) cc_final: 0.8679 (ttmt) REVERT: C 56 ASP cc_start: 0.8625 (p0) cc_final: 0.8412 (p0) REVERT: C 215 LYS cc_start: 0.8944 (tttt) cc_final: 0.8736 (tttp) REVERT: C 231 LEU cc_start: 0.8694 (mt) cc_final: 0.8366 (mt) REVERT: C 261 MET cc_start: 0.8406 (tpp) cc_final: 0.8151 (tpp) REVERT: D 13 LYS cc_start: 0.9013 (tttt) cc_final: 0.8636 (tttm) REVERT: D 17 ASP cc_start: 0.8507 (m-30) cc_final: 0.8258 (m-30) REVERT: D 153 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8087 (mm-30) REVERT: D 190 GLU cc_start: 0.8736 (tt0) cc_final: 0.8409 (tt0) REVERT: D 220 TYR cc_start: 0.8456 (t80) cc_final: 0.8062 (t80) REVERT: D 266 THR cc_start: 0.8814 (p) cc_final: 0.8506 (p) REVERT: E 115 MET cc_start: 0.8829 (ttp) cc_final: 0.8609 (ptm) REVERT: E 190 GLU cc_start: 0.8090 (tt0) cc_final: 0.7767 (tt0) REVERT: E 227 MET cc_start: 0.8455 (mmt) cc_final: 0.8197 (mmt) REVERT: E 284 TYR cc_start: 0.9055 (t80) cc_final: 0.8812 (t80) REVERT: E 424 ASP cc_start: 0.8692 (m-30) cc_final: 0.8483 (t70) REVERT: E 439 ASN cc_start: 0.8401 (m-40) cc_final: 0.8089 (m-40) outliers start: 16 outliers final: 10 residues processed: 469 average time/residue: 0.1421 time to fit residues: 93.4241 Evaluate side-chains 328 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 318 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 268 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0270 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN A 267 HIS A 303 ASN C 90 GLN C 185 GLN C 309 GLN D 267 HIS D 309 GLN E 41 ASN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.114454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.088104 restraints weight = 60679.752| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 4.72 r_work: 0.2976 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14675 Z= 0.128 Angle : 0.613 8.890 20045 Z= 0.308 Chirality : 0.044 0.236 2350 Planarity : 0.005 0.081 2410 Dihedral : 11.107 83.607 2733 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.01 % Allowed : 11.51 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.75 (0.22), residues: 1660 helix: 2.31 (0.20), residues: 620 sheet: 0.54 (0.25), residues: 411 loop : 0.55 (0.30), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 180 TYR 0.028 0.001 TYR D 244 PHE 0.022 0.001 PHE C 293 TRP 0.039 0.001 TRP D 241 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00283 (14630) covalent geometry : angle 0.60193 (19915) SS BOND : bond 0.00285 ( 5) SS BOND : angle 1.92865 ( 10) hydrogen bonds : bond 0.03827 ( 602) hydrogen bonds : angle 4.31077 ( 1678) link_ALPHA1-3 : bond 0.00917 ( 5) link_ALPHA1-3 : angle 2.05427 ( 15) link_ALPHA1-6 : bond 0.00552 ( 5) link_ALPHA1-6 : angle 1.88493 ( 15) link_BETA1-4 : bond 0.00418 ( 15) link_BETA1-4 : angle 1.43798 ( 45) link_NAG-ASN : bond 0.00378 ( 15) link_NAG-ASN : angle 1.18161 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 347 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8386 (mtp) cc_final: 0.7900 (ttm) REVERT: A 14 GLU cc_start: 0.8612 (tt0) cc_final: 0.8352 (pt0) REVERT: A 153 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8715 (mm-30) REVERT: A 163 ASP cc_start: 0.8394 (m-30) cc_final: 0.7995 (m-30) REVERT: A 180 ARG cc_start: 0.8400 (mtm110) cc_final: 0.7972 (mtp-110) REVERT: A 200 PHE cc_start: 0.8703 (m-80) cc_final: 0.8244 (m-80) REVERT: A 297 LEU cc_start: 0.9206 (tp) cc_final: 0.8941 (tt) REVERT: A 303 ASN cc_start: 0.9305 (OUTLIER) cc_final: 0.8993 (m-40) REVERT: B 40 MET cc_start: 0.9093 (mtt) cc_final: 0.8824 (mtt) REVERT: B 52 GLU cc_start: 0.8188 (mp0) cc_final: 0.7939 (mp0) REVERT: B 90 GLN cc_start: 0.8355 (mp10) cc_final: 0.7529 (mp10) REVERT: B 95 ASP cc_start: 0.8707 (p0) cc_final: 0.8398 (p0) REVERT: B 172 ASP cc_start: 0.8749 (m-30) cc_final: 0.8200 (t0) REVERT: B 237 TRP cc_start: 0.8941 (m-10) cc_final: 0.8177 (m-10) REVERT: B 247 SER cc_start: 0.9070 (p) cc_final: 0.8541 (t) REVERT: B 279 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8269 (mtmt) REVERT: B 309 GLN cc_start: 0.7806 (mt0) cc_final: 0.7458 (mp-120) REVERT: B 426 TRP cc_start: 0.8120 (m100) cc_final: 0.7486 (m100) REVERT: C 21 LYS cc_start: 0.9127 (pttt) cc_final: 0.8871 (pttp) REVERT: C 147 GLU cc_start: 0.8978 (tt0) cc_final: 0.8567 (tt0) REVERT: C 163 ASP cc_start: 0.9058 (m-30) cc_final: 0.8714 (m-30) REVERT: C 190 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7811 (tm-30) REVERT: C 213 ARG cc_start: 0.8854 (ttp-110) cc_final: 0.8433 (ptm160) REVERT: C 215 LYS cc_start: 0.8881 (tttt) cc_final: 0.8527 (tttp) REVERT: C 446 TYR cc_start: 0.7043 (m-80) cc_final: 0.6598 (m-10) REVERT: D 55 MET cc_start: 0.9244 (mtp) cc_final: 0.9021 (mtp) REVERT: D 147 GLU cc_start: 0.8686 (tt0) cc_final: 0.8454 (tt0) REVERT: D 153 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8105 (mm-30) REVERT: D 155 GLU cc_start: 0.8844 (tt0) cc_final: 0.8643 (tt0) REVERT: D 190 GLU cc_start: 0.8847 (tt0) cc_final: 0.8431 (tt0) REVERT: D 220 TYR cc_start: 0.8397 (t80) cc_final: 0.8101 (t80) REVERT: E 115 MET cc_start: 0.8920 (ttp) cc_final: 0.8501 (ptm) REVERT: E 147 GLU cc_start: 0.8638 (tt0) cc_final: 0.8409 (tt0) REVERT: E 185 GLN cc_start: 0.8683 (pm20) cc_final: 0.8247 (pm20) REVERT: E 190 GLU cc_start: 0.8708 (tt0) cc_final: 0.8153 (tt0) REVERT: E 227 MET cc_start: 0.8741 (mmt) cc_final: 0.8461 (mmt) REVERT: E 255 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9263 (mt) REVERT: E 284 TYR cc_start: 0.9211 (t80) cc_final: 0.8971 (t80) REVERT: E 424 ASP cc_start: 0.8755 (m-30) cc_final: 0.8514 (t70) outliers start: 30 outliers final: 21 residues processed: 362 average time/residue: 0.1206 time to fit residues: 64.3226 Evaluate side-chains 330 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 307 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.082375 restraints weight = 55057.873| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.36 r_work: 0.2870 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14675 Z= 0.185 Angle : 0.607 8.400 20045 Z= 0.307 Chirality : 0.045 0.206 2350 Planarity : 0.005 0.081 2410 Dihedral : 10.403 78.447 2732 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.21 % Allowed : 12.11 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.46 (0.22), residues: 1660 helix: 2.09 (0.20), residues: 616 sheet: 0.19 (0.25), residues: 439 loop : 0.55 (0.30), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 269 TYR 0.029 0.002 TYR A 299 PHE 0.019 0.001 PHE E 240 TRP 0.037 0.001 TRP D 241 HIS 0.002 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00427 (14630) covalent geometry : angle 0.59668 (19915) SS BOND : bond 0.00141 ( 5) SS BOND : angle 1.43085 ( 10) hydrogen bonds : bond 0.03827 ( 602) hydrogen bonds : angle 4.33467 ( 1678) link_ALPHA1-3 : bond 0.01033 ( 5) link_ALPHA1-3 : angle 1.99790 ( 15) link_ALPHA1-6 : bond 0.00662 ( 5) link_ALPHA1-6 : angle 1.98191 ( 15) link_BETA1-4 : bond 0.00291 ( 15) link_BETA1-4 : angle 1.44400 ( 45) link_NAG-ASN : bond 0.00218 ( 15) link_NAG-ASN : angle 1.23404 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 322 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8438 (mtp) cc_final: 0.7943 (ttm) REVERT: A 153 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8666 (mm-30) REVERT: A 163 ASP cc_start: 0.8392 (m-30) cc_final: 0.8023 (m-30) REVERT: A 172 ASP cc_start: 0.8813 (m-30) cc_final: 0.8245 (t70) REVERT: A 180 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7997 (mtp-110) REVERT: A 190 GLU cc_start: 0.8651 (tt0) cc_final: 0.8420 (tt0) REVERT: A 200 PHE cc_start: 0.8725 (m-80) cc_final: 0.8392 (m-80) REVERT: A 283 MET cc_start: 0.8808 (mmm) cc_final: 0.8566 (tpp) REVERT: A 297 LEU cc_start: 0.9268 (tp) cc_final: 0.9040 (tt) REVERT: A 299 TYR cc_start: 0.9263 (t80) cc_final: 0.9016 (t80) REVERT: B 40 MET cc_start: 0.9101 (mtt) cc_final: 0.8850 (mtt) REVERT: B 55 MET cc_start: 0.8857 (mmt) cc_final: 0.8348 (mmm) REVERT: B 90 GLN cc_start: 0.8458 (mp10) cc_final: 0.7458 (mp10) REVERT: B 95 ASP cc_start: 0.8715 (p0) cc_final: 0.8412 (p0) REVERT: B 172 ASP cc_start: 0.8740 (m-30) cc_final: 0.8192 (t0) REVERT: B 247 SER cc_start: 0.9077 (p) cc_final: 0.8564 (t) REVERT: B 426 TRP cc_start: 0.8180 (m100) cc_final: 0.7517 (m100) REVERT: C 21 LYS cc_start: 0.9145 (pttt) cc_final: 0.8858 (pttp) REVERT: C 190 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7672 (tm-30) REVERT: C 215 LYS cc_start: 0.8933 (tttt) cc_final: 0.8610 (tttp) REVERT: C 446 TYR cc_start: 0.7080 (m-80) cc_final: 0.6709 (m-10) REVERT: D 153 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8018 (mm-30) REVERT: D 190 GLU cc_start: 0.8881 (tt0) cc_final: 0.8449 (tt0) REVERT: D 220 TYR cc_start: 0.8442 (t80) cc_final: 0.8151 (t80) REVERT: E 185 GLN cc_start: 0.8722 (pm20) cc_final: 0.8242 (pm20) REVERT: E 190 GLU cc_start: 0.8841 (tt0) cc_final: 0.8514 (tt0) REVERT: E 424 ASP cc_start: 0.8829 (m-30) cc_final: 0.8546 (t70) outliers start: 33 outliers final: 29 residues processed: 343 average time/residue: 0.1159 time to fit residues: 59.0871 Evaluate side-chains 324 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 295 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 265 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 114 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 145 optimal weight: 0.0010 chunk 151 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.084090 restraints weight = 54253.927| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.34 r_work: 0.2900 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14675 Z= 0.122 Angle : 0.592 8.391 20045 Z= 0.294 Chirality : 0.044 0.230 2350 Planarity : 0.004 0.079 2410 Dihedral : 9.561 73.054 2730 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.47 % Allowed : 13.38 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.49 (0.22), residues: 1660 helix: 2.04 (0.20), residues: 620 sheet: 0.53 (0.25), residues: 409 loop : 0.38 (0.29), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 180 TYR 0.021 0.001 TYR E 299 PHE 0.019 0.001 PHE E 240 TRP 0.052 0.001 TRP D 241 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00274 (14630) covalent geometry : angle 0.58250 (19915) SS BOND : bond 0.00223 ( 5) SS BOND : angle 0.88112 ( 10) hydrogen bonds : bond 0.03567 ( 602) hydrogen bonds : angle 4.27298 ( 1678) link_ALPHA1-3 : bond 0.01166 ( 5) link_ALPHA1-3 : angle 2.09127 ( 15) link_ALPHA1-6 : bond 0.00841 ( 5) link_ALPHA1-6 : angle 1.97933 ( 15) link_BETA1-4 : bond 0.00344 ( 15) link_BETA1-4 : angle 1.32677 ( 45) link_NAG-ASN : bond 0.00239 ( 15) link_NAG-ASN : angle 1.16618 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 320 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8424 (mtp) cc_final: 0.7919 (ttm) REVERT: A 14 GLU cc_start: 0.8580 (tt0) cc_final: 0.8318 (pt0) REVERT: A 155 GLU cc_start: 0.8728 (tt0) cc_final: 0.8501 (tt0) REVERT: A 163 ASP cc_start: 0.8260 (m-30) cc_final: 0.7889 (m-30) REVERT: A 172 ASP cc_start: 0.8774 (m-30) cc_final: 0.8280 (t70) REVERT: A 180 ARG cc_start: 0.8309 (mtm110) cc_final: 0.8056 (mtp-110) REVERT: A 200 PHE cc_start: 0.8755 (m-80) cc_final: 0.8329 (m-80) REVERT: A 297 LEU cc_start: 0.9157 (tp) cc_final: 0.8921 (tt) REVERT: A 299 TYR cc_start: 0.9302 (t80) cc_final: 0.9045 (t80) REVERT: B 40 MET cc_start: 0.9099 (mtt) cc_final: 0.8843 (mtt) REVERT: B 55 MET cc_start: 0.8939 (mmt) cc_final: 0.8329 (mmm) REVERT: B 90 GLN cc_start: 0.8499 (mp10) cc_final: 0.8197 (mp10) REVERT: B 95 ASP cc_start: 0.8726 (p0) cc_final: 0.8498 (p0) REVERT: B 172 ASP cc_start: 0.8619 (m-30) cc_final: 0.8114 (t0) REVERT: B 237 TRP cc_start: 0.8927 (m-10) cc_final: 0.7892 (m-10) REVERT: B 247 SER cc_start: 0.9045 (p) cc_final: 0.8521 (t) REVERT: B 298 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7669 (tm-30) REVERT: B 426 TRP cc_start: 0.8135 (m100) cc_final: 0.7565 (m100) REVERT: C 13 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8553 (ttmm) REVERT: C 21 LYS cc_start: 0.9084 (pttt) cc_final: 0.8818 (pttp) REVERT: C 163 ASP cc_start: 0.9048 (m-30) cc_final: 0.8701 (m-30) REVERT: C 190 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 215 LYS cc_start: 0.8898 (tttt) cc_final: 0.8556 (tttp) REVERT: C 446 TYR cc_start: 0.7038 (m-80) cc_final: 0.6747 (m-10) REVERT: D 55 MET cc_start: 0.9341 (mtp) cc_final: 0.9118 (mmm) REVERT: D 153 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8032 (mm-30) REVERT: D 190 GLU cc_start: 0.8876 (tt0) cc_final: 0.8395 (tt0) REVERT: E 185 GLN cc_start: 0.8736 (pm20) cc_final: 0.8530 (pm20) REVERT: E 190 GLU cc_start: 0.8926 (tt0) cc_final: 0.8680 (tt0) REVERT: E 227 MET cc_start: 0.8706 (mmt) cc_final: 0.8453 (mmp) REVERT: E 424 ASP cc_start: 0.8780 (m-30) cc_final: 0.8536 (t70) outliers start: 37 outliers final: 32 residues processed: 341 average time/residue: 0.1105 time to fit residues: 57.0338 Evaluate side-chains 332 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 163 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN E 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.106805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.082552 restraints weight = 45898.813| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.00 r_work: 0.2890 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14675 Z= 0.184 Angle : 0.612 8.811 20045 Z= 0.306 Chirality : 0.045 0.242 2350 Planarity : 0.005 0.080 2410 Dihedral : 9.194 69.926 2730 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.34 % Allowed : 14.05 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.38 (0.22), residues: 1660 helix: 1.94 (0.20), residues: 620 sheet: 0.50 (0.26), residues: 405 loop : 0.30 (0.28), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 180 TYR 0.029 0.002 TYR E 299 PHE 0.028 0.002 PHE B 438 TRP 0.038 0.001 TRP D 241 HIS 0.002 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00428 (14630) covalent geometry : angle 0.60152 (19915) SS BOND : bond 0.00245 ( 5) SS BOND : angle 1.12672 ( 10) hydrogen bonds : bond 0.03736 ( 602) hydrogen bonds : angle 4.34066 ( 1678) link_ALPHA1-3 : bond 0.01162 ( 5) link_ALPHA1-3 : angle 2.16334 ( 15) link_ALPHA1-6 : bond 0.00825 ( 5) link_ALPHA1-6 : angle 2.03257 ( 15) link_BETA1-4 : bond 0.00304 ( 15) link_BETA1-4 : angle 1.37862 ( 45) link_NAG-ASN : bond 0.00182 ( 15) link_NAG-ASN : angle 1.26569 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 310 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8455 (mtp) cc_final: 0.8003 (ttm) REVERT: A 14 GLU cc_start: 0.8610 (tt0) cc_final: 0.8323 (pt0) REVERT: A 163 ASP cc_start: 0.8267 (m-30) cc_final: 0.7926 (m-30) REVERT: A 172 ASP cc_start: 0.8817 (m-30) cc_final: 0.8509 (t70) REVERT: A 200 PHE cc_start: 0.8737 (m-80) cc_final: 0.8339 (m-80) REVERT: A 297 LEU cc_start: 0.9187 (tp) cc_final: 0.8942 (tt) REVERT: B 40 MET cc_start: 0.9114 (mtt) cc_final: 0.8878 (mtt) REVERT: B 52 GLU cc_start: 0.8073 (mp0) cc_final: 0.7522 (mp0) REVERT: B 55 MET cc_start: 0.8930 (mmt) cc_final: 0.8297 (mmm) REVERT: B 90 GLN cc_start: 0.8495 (mp10) cc_final: 0.8177 (mp10) REVERT: B 95 ASP cc_start: 0.8660 (p0) cc_final: 0.8374 (p0) REVERT: B 155 GLU cc_start: 0.9030 (tt0) cc_final: 0.8594 (tt0) REVERT: B 172 ASP cc_start: 0.8563 (m-30) cc_final: 0.7987 (t0) REVERT: B 224 GLN cc_start: 0.8259 (tp-100) cc_final: 0.7683 (tp40) REVERT: B 247 SER cc_start: 0.9054 (p) cc_final: 0.8531 (t) REVERT: B 426 TRP cc_start: 0.8194 (m100) cc_final: 0.7614 (m100) REVERT: C 13 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8538 (ttmm) REVERT: C 21 LYS cc_start: 0.9072 (pttt) cc_final: 0.8788 (pttp) REVERT: C 190 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7537 (tm-30) REVERT: C 215 LYS cc_start: 0.8869 (tttt) cc_final: 0.8506 (tttp) REVERT: C 226 TYR cc_start: 0.9004 (m-80) cc_final: 0.8799 (m-80) REVERT: C 446 TYR cc_start: 0.7040 (m-80) cc_final: 0.6760 (m-10) REVERT: D 153 GLU cc_start: 0.8836 (mm-30) cc_final: 0.7929 (mm-30) REVERT: D 190 GLU cc_start: 0.8882 (tt0) cc_final: 0.8452 (tt0) REVERT: E 147 GLU cc_start: 0.8806 (tt0) cc_final: 0.8582 (tt0) REVERT: E 182 GLU cc_start: 0.8693 (tp30) cc_final: 0.8404 (tp30) REVERT: E 185 GLN cc_start: 0.8769 (pm20) cc_final: 0.8289 (pm20) REVERT: E 190 GLU cc_start: 0.8858 (tt0) cc_final: 0.8596 (tt0) REVERT: E 424 ASP cc_start: 0.8824 (m-30) cc_final: 0.8512 (t70) outliers start: 35 outliers final: 29 residues processed: 330 average time/residue: 0.1177 time to fit residues: 58.2597 Evaluate side-chains 321 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 292 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 282 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.083601 restraints weight = 53753.375| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 4.38 r_work: 0.2895 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14675 Z= 0.125 Angle : 0.611 8.691 20045 Z= 0.301 Chirality : 0.045 0.247 2350 Planarity : 0.004 0.080 2410 Dihedral : 8.754 67.238 2728 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.21 % Allowed : 14.45 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 (0.22), residues: 1660 helix: 1.99 (0.20), residues: 620 sheet: 0.55 (0.26), residues: 405 loop : 0.32 (0.28), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 180 TYR 0.033 0.001 TYR A 299 PHE 0.025 0.001 PHE C 293 TRP 0.064 0.001 TRP D 241 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00281 (14630) covalent geometry : angle 0.60177 (19915) SS BOND : bond 0.00211 ( 5) SS BOND : angle 0.81283 ( 10) hydrogen bonds : bond 0.03621 ( 602) hydrogen bonds : angle 4.32098 ( 1678) link_ALPHA1-3 : bond 0.01181 ( 5) link_ALPHA1-3 : angle 2.15115 ( 15) link_ALPHA1-6 : bond 0.00923 ( 5) link_ALPHA1-6 : angle 1.94680 ( 15) link_BETA1-4 : bond 0.00351 ( 15) link_BETA1-4 : angle 1.29202 ( 45) link_NAG-ASN : bond 0.00226 ( 15) link_NAG-ASN : angle 1.19415 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 311 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8440 (mtp) cc_final: 0.7962 (ttm) REVERT: A 14 GLU cc_start: 0.8608 (tt0) cc_final: 0.8331 (pt0) REVERT: A 163 ASP cc_start: 0.8274 (m-30) cc_final: 0.7924 (m-30) REVERT: A 172 ASP cc_start: 0.8843 (m-30) cc_final: 0.8544 (t70) REVERT: A 200 PHE cc_start: 0.8777 (m-80) cc_final: 0.8387 (m-80) REVERT: A 297 LEU cc_start: 0.9150 (tp) cc_final: 0.8908 (tt) REVERT: B 52 GLU cc_start: 0.8161 (mp0) cc_final: 0.7641 (mp0) REVERT: B 55 MET cc_start: 0.8977 (mmt) cc_final: 0.8325 (mmm) REVERT: B 90 GLN cc_start: 0.8531 (mp10) cc_final: 0.8217 (mp10) REVERT: B 95 ASP cc_start: 0.8676 (p0) cc_final: 0.8407 (p0) REVERT: B 155 GLU cc_start: 0.9115 (tt0) cc_final: 0.8721 (tt0) REVERT: B 172 ASP cc_start: 0.8631 (m-30) cc_final: 0.8046 (t0) REVERT: B 235 LEU cc_start: 0.9406 (tp) cc_final: 0.9206 (tt) REVERT: B 237 TRP cc_start: 0.8940 (m-10) cc_final: 0.7861 (m-10) REVERT: B 247 SER cc_start: 0.8995 (p) cc_final: 0.8453 (t) REVERT: B 298 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7737 (tm-30) REVERT: B 426 TRP cc_start: 0.8173 (m100) cc_final: 0.7655 (m100) REVERT: C 9 MET cc_start: 0.8796 (mtp) cc_final: 0.8013 (ttm) REVERT: C 13 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8551 (ttmm) REVERT: C 21 LYS cc_start: 0.9024 (pttt) cc_final: 0.8741 (pttp) REVERT: C 190 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7582 (tm-30) REVERT: C 215 LYS cc_start: 0.8873 (tttt) cc_final: 0.8524 (tttp) REVERT: C 446 TYR cc_start: 0.7078 (m-80) cc_final: 0.6811 (m-10) REVERT: D 55 MET cc_start: 0.9278 (mtp) cc_final: 0.8810 (mtp) REVERT: D 153 GLU cc_start: 0.8888 (mm-30) cc_final: 0.7944 (mm-30) REVERT: D 190 GLU cc_start: 0.8902 (tt0) cc_final: 0.8437 (tt0) REVERT: D 294 LEU cc_start: 0.9032 (mm) cc_final: 0.8832 (mt) REVERT: E 147 GLU cc_start: 0.8800 (tt0) cc_final: 0.8533 (tt0) REVERT: E 182 GLU cc_start: 0.8706 (tp30) cc_final: 0.8413 (tp30) REVERT: E 185 GLN cc_start: 0.8769 (pm20) cc_final: 0.8295 (pm20) REVERT: E 190 GLU cc_start: 0.8884 (tt0) cc_final: 0.8670 (tt0) REVERT: E 424 ASP cc_start: 0.8796 (m-30) cc_final: 0.8571 (t70) outliers start: 33 outliers final: 31 residues processed: 331 average time/residue: 0.1199 time to fit residues: 59.3998 Evaluate side-chains 328 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 126 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.107927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.084087 restraints weight = 37994.664| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.66 r_work: 0.2920 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14675 Z= 0.158 Angle : 0.629 10.174 20045 Z= 0.310 Chirality : 0.046 0.367 2350 Planarity : 0.005 0.080 2410 Dihedral : 8.466 65.012 2728 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.27 % Allowed : 14.98 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.39 (0.22), residues: 1660 helix: 1.95 (0.20), residues: 620 sheet: 0.53 (0.26), residues: 405 loop : 0.28 (0.28), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 180 TYR 0.029 0.001 TYR A 299 PHE 0.028 0.001 PHE E 240 TRP 0.057 0.001 TRP D 241 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00364 (14630) covalent geometry : angle 0.61968 (19915) SS BOND : bond 0.00212 ( 5) SS BOND : angle 0.95121 ( 10) hydrogen bonds : bond 0.03671 ( 602) hydrogen bonds : angle 4.34761 ( 1678) link_ALPHA1-3 : bond 0.01173 ( 5) link_ALPHA1-3 : angle 2.15997 ( 15) link_ALPHA1-6 : bond 0.00911 ( 5) link_ALPHA1-6 : angle 1.95800 ( 15) link_BETA1-4 : bond 0.00338 ( 15) link_BETA1-4 : angle 1.32071 ( 45) link_NAG-ASN : bond 0.00193 ( 15) link_NAG-ASN : angle 1.26998 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 301 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8421 (mtp) cc_final: 0.7979 (ttm) REVERT: A 14 GLU cc_start: 0.8612 (tt0) cc_final: 0.8330 (pt0) REVERT: A 163 ASP cc_start: 0.8258 (m-30) cc_final: 0.7925 (m-30) REVERT: A 172 ASP cc_start: 0.8799 (m-30) cc_final: 0.8477 (t70) REVERT: A 200 PHE cc_start: 0.8756 (m-80) cc_final: 0.8384 (m-80) REVERT: A 297 LEU cc_start: 0.9144 (tp) cc_final: 0.8897 (tt) REVERT: B 52 GLU cc_start: 0.8128 (mp0) cc_final: 0.7608 (mp0) REVERT: B 55 MET cc_start: 0.8990 (mmt) cc_final: 0.8374 (mmm) REVERT: B 90 GLN cc_start: 0.8544 (mp10) cc_final: 0.8224 (mp10) REVERT: B 95 ASP cc_start: 0.8641 (p0) cc_final: 0.8384 (p0) REVERT: B 155 GLU cc_start: 0.9042 (tt0) cc_final: 0.8642 (tt0) REVERT: B 172 ASP cc_start: 0.8568 (m-30) cc_final: 0.8001 (t0) REVERT: B 224 GLN cc_start: 0.8112 (tp40) cc_final: 0.7588 (tp40) REVERT: B 247 SER cc_start: 0.8992 (p) cc_final: 0.8449 (t) REVERT: B 426 TRP cc_start: 0.8198 (m100) cc_final: 0.7661 (m100) REVERT: C 9 MET cc_start: 0.8709 (mtp) cc_final: 0.8239 (ttm) REVERT: C 13 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8649 (ttmm) REVERT: C 21 LYS cc_start: 0.9009 (pttt) cc_final: 0.8724 (pttp) REVERT: C 190 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 215 LYS cc_start: 0.8801 (tttt) cc_final: 0.8387 (tttp) REVERT: C 231 LEU cc_start: 0.8025 (mm) cc_final: 0.7502 (tp) REVERT: C 446 TYR cc_start: 0.7151 (m-80) cc_final: 0.6918 (m-10) REVERT: D 55 MET cc_start: 0.9168 (mtp) cc_final: 0.8836 (mtp) REVERT: D 153 GLU cc_start: 0.8819 (mm-30) cc_final: 0.7859 (mm-30) REVERT: D 190 GLU cc_start: 0.8857 (tt0) cc_final: 0.8502 (tt0) REVERT: D 428 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7723 (mtt-85) REVERT: E 182 GLU cc_start: 0.8699 (tp30) cc_final: 0.8425 (tp30) REVERT: E 185 GLN cc_start: 0.8729 (pm20) cc_final: 0.8358 (pm20) REVERT: E 190 GLU cc_start: 0.8780 (tt0) cc_final: 0.8569 (tt0) REVERT: E 424 ASP cc_start: 0.8791 (m-30) cc_final: 0.8543 (t70) outliers start: 34 outliers final: 28 residues processed: 324 average time/residue: 0.1180 time to fit residues: 57.8145 Evaluate side-chains 320 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 282 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.084006 restraints weight = 44503.971| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.99 r_work: 0.2914 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14675 Z= 0.141 Angle : 0.645 11.136 20045 Z= 0.315 Chirality : 0.046 0.369 2350 Planarity : 0.004 0.080 2410 Dihedral : 8.143 62.563 2728 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.21 % Allowed : 15.25 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.36 (0.22), residues: 1660 helix: 1.85 (0.20), residues: 620 sheet: 0.41 (0.25), residues: 445 loop : 0.44 (0.29), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 180 TYR 0.028 0.001 TYR A 299 PHE 0.025 0.001 PHE E 240 TRP 0.046 0.001 TRP D 241 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00322 (14630) covalent geometry : angle 0.63648 (19915) SS BOND : bond 0.00238 ( 5) SS BOND : angle 1.16611 ( 10) hydrogen bonds : bond 0.03673 ( 602) hydrogen bonds : angle 4.34749 ( 1678) link_ALPHA1-3 : bond 0.01202 ( 5) link_ALPHA1-3 : angle 2.13361 ( 15) link_ALPHA1-6 : bond 0.00971 ( 5) link_ALPHA1-6 : angle 1.88274 ( 15) link_BETA1-4 : bond 0.00362 ( 15) link_BETA1-4 : angle 1.28455 ( 45) link_NAG-ASN : bond 0.00199 ( 15) link_NAG-ASN : angle 1.24823 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 299 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8413 (mtp) cc_final: 0.7977 (ttm) REVERT: A 14 GLU cc_start: 0.8613 (tt0) cc_final: 0.8332 (pt0) REVERT: A 163 ASP cc_start: 0.8282 (m-30) cc_final: 0.7938 (m-30) REVERT: A 172 ASP cc_start: 0.8815 (m-30) cc_final: 0.8487 (t70) REVERT: A 180 ARG cc_start: 0.8427 (mtp-110) cc_final: 0.7981 (ttp80) REVERT: A 200 PHE cc_start: 0.8767 (m-80) cc_final: 0.8358 (m-80) REVERT: A 297 LEU cc_start: 0.9143 (tp) cc_final: 0.8891 (tt) REVERT: B 52 GLU cc_start: 0.8141 (mp0) cc_final: 0.7891 (mp0) REVERT: B 55 MET cc_start: 0.9004 (mmt) cc_final: 0.8395 (mmm) REVERT: B 90 GLN cc_start: 0.8545 (mp10) cc_final: 0.8224 (mp10) REVERT: B 95 ASP cc_start: 0.8669 (p0) cc_final: 0.8414 (p0) REVERT: B 155 GLU cc_start: 0.9070 (tt0) cc_final: 0.8675 (tt0) REVERT: B 172 ASP cc_start: 0.8600 (m-30) cc_final: 0.7715 (t0) REVERT: B 173 LYS cc_start: 0.9416 (mtmm) cc_final: 0.8955 (mppt) REVERT: B 224 GLN cc_start: 0.7985 (tp40) cc_final: 0.7347 (tp40) REVERT: B 247 SER cc_start: 0.8982 (p) cc_final: 0.8430 (t) REVERT: B 298 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7801 (tm-30) REVERT: B 426 TRP cc_start: 0.8146 (m100) cc_final: 0.7592 (m100) REVERT: C 9 MET cc_start: 0.8606 (mtp) cc_final: 0.8113 (ttm) REVERT: C 13 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8672 (ttmm) REVERT: C 21 LYS cc_start: 0.8986 (pttt) cc_final: 0.8705 (pttp) REVERT: C 163 ASP cc_start: 0.9026 (m-30) cc_final: 0.8654 (m-30) REVERT: C 190 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7518 (tm-30) REVERT: C 215 LYS cc_start: 0.8847 (tttt) cc_final: 0.8481 (tttp) REVERT: C 231 LEU cc_start: 0.8092 (mm) cc_final: 0.7549 (tp) REVERT: C 298 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8536 (tm-30) REVERT: C 446 TYR cc_start: 0.7214 (m-80) cc_final: 0.6978 (m-10) REVERT: D 55 MET cc_start: 0.9224 (mtp) cc_final: 0.8812 (mtp) REVERT: D 153 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8099 (mm-30) REVERT: D 190 GLU cc_start: 0.8884 (tt0) cc_final: 0.8505 (tt0) REVERT: D 428 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7724 (mtt-85) REVERT: E 182 GLU cc_start: 0.8703 (tp30) cc_final: 0.8412 (tp30) REVERT: E 185 GLN cc_start: 0.8739 (pm20) cc_final: 0.8412 (pm20) REVERT: E 190 GLU cc_start: 0.8829 (tt0) cc_final: 0.8603 (tt0) REVERT: E 424 ASP cc_start: 0.8767 (m-30) cc_final: 0.8524 (t70) outliers start: 33 outliers final: 31 residues processed: 317 average time/residue: 0.1218 time to fit residues: 57.8636 Evaluate side-chains 324 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 293 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.083936 restraints weight = 46793.012| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.08 r_work: 0.2907 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14675 Z= 0.140 Angle : 0.644 11.019 20045 Z= 0.315 Chirality : 0.046 0.360 2350 Planarity : 0.004 0.080 2410 Dihedral : 7.889 60.491 2728 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.34 % Allowed : 15.25 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.37 (0.22), residues: 1660 helix: 1.85 (0.20), residues: 620 sheet: 0.42 (0.25), residues: 445 loop : 0.45 (0.29), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 180 TYR 0.028 0.001 TYR A 299 PHE 0.024 0.001 PHE C 293 TRP 0.040 0.001 TRP D 241 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00323 (14630) covalent geometry : angle 0.63572 (19915) SS BOND : bond 0.00214 ( 5) SS BOND : angle 1.07097 ( 10) hydrogen bonds : bond 0.03635 ( 602) hydrogen bonds : angle 4.34615 ( 1678) link_ALPHA1-3 : bond 0.01166 ( 5) link_ALPHA1-3 : angle 2.12708 ( 15) link_ALPHA1-6 : bond 0.00991 ( 5) link_ALPHA1-6 : angle 1.83625 ( 15) link_BETA1-4 : bond 0.00369 ( 15) link_BETA1-4 : angle 1.27287 ( 45) link_NAG-ASN : bond 0.00199 ( 15) link_NAG-ASN : angle 1.24853 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 299 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8406 (mtp) cc_final: 0.7965 (ttm) REVERT: A 14 GLU cc_start: 0.8629 (tt0) cc_final: 0.8349 (pt0) REVERT: A 163 ASP cc_start: 0.8289 (m-30) cc_final: 0.7943 (m-30) REVERT: A 172 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8488 (t70) REVERT: A 180 ARG cc_start: 0.8506 (mtp-110) cc_final: 0.8081 (ttp80) REVERT: A 200 PHE cc_start: 0.8795 (m-80) cc_final: 0.8403 (m-80) REVERT: A 297 LEU cc_start: 0.9140 (tp) cc_final: 0.8893 (tt) REVERT: B 52 GLU cc_start: 0.8178 (mp0) cc_final: 0.7941 (mp0) REVERT: B 55 MET cc_start: 0.9015 (mmt) cc_final: 0.8432 (mmm) REVERT: B 90 GLN cc_start: 0.8549 (mp10) cc_final: 0.8228 (mp10) REVERT: B 95 ASP cc_start: 0.8683 (p0) cc_final: 0.8427 (p0) REVERT: B 172 ASP cc_start: 0.8609 (m-30) cc_final: 0.7724 (t0) REVERT: B 173 LYS cc_start: 0.9420 (mtmm) cc_final: 0.8960 (mppt) REVERT: B 224 GLN cc_start: 0.7973 (tp40) cc_final: 0.7372 (tp40) REVERT: B 247 SER cc_start: 0.8973 (p) cc_final: 0.8423 (t) REVERT: B 298 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7837 (tm-30) REVERT: B 426 TRP cc_start: 0.8170 (m100) cc_final: 0.7642 (m100) REVERT: C 9 MET cc_start: 0.8608 (mtp) cc_final: 0.8190 (ttm) REVERT: C 13 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8516 (ttmm) REVERT: C 21 LYS cc_start: 0.8990 (pttt) cc_final: 0.8703 (pttp) REVERT: C 190 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7568 (tm-30) REVERT: C 215 LYS cc_start: 0.8900 (tttt) cc_final: 0.8545 (tttp) REVERT: C 231 LEU cc_start: 0.8084 (mm) cc_final: 0.7553 (tp) REVERT: C 298 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8547 (tm-30) REVERT: C 446 TYR cc_start: 0.7204 (m-80) cc_final: 0.7003 (m-10) REVERT: D 55 MET cc_start: 0.9229 (mtp) cc_final: 0.8831 (mtp) REVERT: D 153 GLU cc_start: 0.8857 (mm-30) cc_final: 0.7883 (mm-30) REVERT: D 190 GLU cc_start: 0.8901 (tt0) cc_final: 0.8517 (tt0) REVERT: E 182 GLU cc_start: 0.8685 (tp30) cc_final: 0.8391 (tp30) REVERT: E 185 GLN cc_start: 0.8744 (pm20) cc_final: 0.8443 (pm20) REVERT: E 190 GLU cc_start: 0.8854 (tt0) cc_final: 0.8640 (tt0) outliers start: 35 outliers final: 32 residues processed: 319 average time/residue: 0.1170 time to fit residues: 56.1371 Evaluate side-chains 327 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 0.0570 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 0.0770 chunk 67 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.109802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.085520 restraints weight = 46267.155| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 4.05 r_work: 0.2935 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14675 Z= 0.121 Angle : 0.642 10.868 20045 Z= 0.311 Chirality : 0.045 0.352 2350 Planarity : 0.004 0.081 2410 Dihedral : 7.480 58.975 2728 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.07 % Allowed : 15.72 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.40 (0.22), residues: 1660 helix: 1.85 (0.20), residues: 621 sheet: 0.28 (0.25), residues: 469 loop : 0.68 (0.30), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 180 TYR 0.029 0.001 TYR A 299 PHE 0.024 0.001 PHE C 293 TRP 0.046 0.001 TRP D 241 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00273 (14630) covalent geometry : angle 0.63453 (19915) SS BOND : bond 0.00166 ( 5) SS BOND : angle 0.86099 ( 10) hydrogen bonds : bond 0.03516 ( 602) hydrogen bonds : angle 4.30589 ( 1678) link_ALPHA1-3 : bond 0.01158 ( 5) link_ALPHA1-3 : angle 2.05547 ( 15) link_ALPHA1-6 : bond 0.01061 ( 5) link_ALPHA1-6 : angle 1.75244 ( 15) link_BETA1-4 : bond 0.00424 ( 15) link_BETA1-4 : angle 1.21999 ( 45) link_NAG-ASN : bond 0.00212 ( 15) link_NAG-ASN : angle 1.23288 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 314 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8361 (mtp) cc_final: 0.7914 (ttm) REVERT: A 14 GLU cc_start: 0.8639 (tt0) cc_final: 0.8382 (pt0) REVERT: A 68 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8062 (ttt-90) REVERT: A 163 ASP cc_start: 0.8149 (m-30) cc_final: 0.7748 (m-30) REVERT: A 172 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8466 (t70) REVERT: A 180 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.8076 (ttp80) REVERT: A 200 PHE cc_start: 0.8785 (m-80) cc_final: 0.8326 (m-80) REVERT: A 297 LEU cc_start: 0.9146 (tp) cc_final: 0.8896 (tt) REVERT: B 52 GLU cc_start: 0.8160 (mp0) cc_final: 0.7936 (mp0) REVERT: B 55 MET cc_start: 0.9021 (mmt) cc_final: 0.8446 (mmm) REVERT: B 90 GLN cc_start: 0.8548 (mp10) cc_final: 0.8227 (mp10) REVERT: B 95 ASP cc_start: 0.8639 (p0) cc_final: 0.8358 (p0) REVERT: B 172 ASP cc_start: 0.8604 (m-30) cc_final: 0.7977 (t0) REVERT: B 173 LYS cc_start: 0.9400 (mtmm) cc_final: 0.9024 (mppt) REVERT: B 224 GLN cc_start: 0.7979 (tp40) cc_final: 0.7408 (tp40) REVERT: B 237 TRP cc_start: 0.8897 (m-10) cc_final: 0.8000 (m-10) REVERT: B 247 SER cc_start: 0.8951 (p) cc_final: 0.8397 (t) REVERT: B 298 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7810 (tm-30) REVERT: B 426 TRP cc_start: 0.8116 (m100) cc_final: 0.7620 (m100) REVERT: C 9 MET cc_start: 0.8592 (mtp) cc_final: 0.8159 (ttm) REVERT: C 13 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8546 (ttmm) REVERT: C 21 LYS cc_start: 0.8987 (pttt) cc_final: 0.8701 (pttp) REVERT: C 163 ASP cc_start: 0.9045 (m-30) cc_final: 0.8689 (m-30) REVERT: C 190 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7549 (tm-30) REVERT: C 215 LYS cc_start: 0.8877 (tttt) cc_final: 0.8529 (tttp) REVERT: C 231 LEU cc_start: 0.8067 (mm) cc_final: 0.7526 (tp) REVERT: C 261 MET cc_start: 0.8367 (ttt) cc_final: 0.8125 (ttt) REVERT: C 298 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8570 (tm-30) REVERT: C 446 TYR cc_start: 0.7237 (m-80) cc_final: 0.6890 (m-10) REVERT: D 55 MET cc_start: 0.9189 (mtp) cc_final: 0.8811 (mtp) REVERT: D 153 GLU cc_start: 0.8834 (mm-30) cc_final: 0.7866 (mm-30) REVERT: D 190 GLU cc_start: 0.8880 (tt0) cc_final: 0.8495 (tt0) REVERT: D 222 ILE cc_start: 0.9380 (mm) cc_final: 0.9141 (tp) REVERT: E 147 GLU cc_start: 0.8619 (tt0) cc_final: 0.8372 (tt0) REVERT: E 182 GLU cc_start: 0.8654 (tp30) cc_final: 0.8357 (tp30) REVERT: E 185 GLN cc_start: 0.8719 (pm20) cc_final: 0.8403 (pm20) REVERT: E 190 GLU cc_start: 0.8803 (tt0) cc_final: 0.8576 (tt0) outliers start: 31 outliers final: 29 residues processed: 332 average time/residue: 0.1225 time to fit residues: 60.6036 Evaluate side-chains 331 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 301 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 2 optimal weight: 0.0870 chunk 48 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.084629 restraints weight = 53056.389| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 4.32 r_work: 0.2912 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14675 Z= 0.134 Angle : 0.651 10.672 20045 Z= 0.315 Chirality : 0.045 0.352 2350 Planarity : 0.004 0.080 2410 Dihedral : 7.300 59.853 2728 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.01 % Allowed : 16.32 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 (0.22), residues: 1660 helix: 1.87 (0.20), residues: 621 sheet: 0.31 (0.25), residues: 469 loop : 0.70 (0.30), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 428 TYR 0.029 0.001 TYR A 299 PHE 0.030 0.001 PHE A 31 TRP 0.044 0.001 TRP D 241 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00311 (14630) covalent geometry : angle 0.64345 (19915) SS BOND : bond 0.00219 ( 5) SS BOND : angle 0.94714 ( 10) hydrogen bonds : bond 0.03493 ( 602) hydrogen bonds : angle 4.27793 ( 1678) link_ALPHA1-3 : bond 0.01126 ( 5) link_ALPHA1-3 : angle 2.04323 ( 15) link_ALPHA1-6 : bond 0.01041 ( 5) link_ALPHA1-6 : angle 1.73310 ( 15) link_BETA1-4 : bond 0.00408 ( 15) link_BETA1-4 : angle 1.23880 ( 45) link_NAG-ASN : bond 0.00196 ( 15) link_NAG-ASN : angle 1.26275 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3721.96 seconds wall clock time: 64 minutes 38.54 seconds (3878.54 seconds total)