Starting phenix.real_space_refine on Tue Nov 18 13:05:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ff0_50347/11_2025/9ff0_50347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ff0_50347/11_2025/9ff0_50347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ff0_50347/11_2025/9ff0_50347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ff0_50347/11_2025/9ff0_50347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ff0_50347/11_2025/9ff0_50347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ff0_50347/11_2025/9ff0_50347.map" } resolution = 3.4 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 9366 2.51 5 N 2297 2.21 5 O 2641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14384 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2821 Chain: "B" Number of atoms: 2757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Chain: "C" Number of atoms: 2774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2765 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 321} Conformer: "B" Number of residues, atoms: 338, 2765 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 321} bond proxies already assigned to first conformer: 2829 Chain: "D" Number of atoms: 2766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2821 Chain: "E" Number of atoms: 2766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2821 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: 5.44, per 1000 atoms: 0.38 Number of scatterers: 14384 At special positions: 0 Unit cell: (100.434, 100.434, 131.432, 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 2641 8.00 N 2297 7.00 C 9366 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: 1.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3210 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 15 sheets defined 42.2% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 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 91 removed outlier: 3.591A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (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 239 removed outlier: 3.972A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 246 through 268 Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 309 through 446 removed outlier: 3.671A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'B' and resid 8 through 20 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.576A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.331A 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 239 removed outlier: 4.070A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 270 removed outlier: 4.182A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 305 removed outlier: 3.721A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 446 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 8 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 223 Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.675A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.773A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 271 removed outlier: 3.604A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 306 Processing helix chain 'C' and resid 309 through 447 removed outlier: 3.853A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 139 through 143 removed outlier: 4.401A 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: 3.874A 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 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 246 through 272 removed outlier: 3.922A pdb=" N ARG D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 305 removed outlier: 3.572A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 446 removed outlier: 3.859A 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 8 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 239 removed outlier: 4.076A pdb=" N SER E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) 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 247 through 270 Processing helix chain 'E' and resid 279 through 307 removed outlier: 4.334A pdb=" N PHE E 307 " --> pdb=" O ASN E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 447 Proline residue: E 432 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.133A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.296A pdb=" N ASP A 101 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ALA A 135 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A 103 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 42 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 4.041A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL A 199 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A 205 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN A 197 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG A 207 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER A 195 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER A 209 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A 193 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER A 211 " --> pdb=" O HIS A 191 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS A 191 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG A 213 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.349A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 106 removed outlier: 7.212A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.024A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.357A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR C 60 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE C 47 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N TYR C 62 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ALA C 45 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLN C 64 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASP C 43 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR C 66 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASN C 41 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N ARG C 68 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N GLY C 39 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.388A pdb=" N ASP C 101 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA C 135 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS C 103 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR C 60 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE C 47 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N TYR C 62 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ALA C 45 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLN C 64 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASP C 43 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR C 66 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASN C 41 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N ARG C 68 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N GLY C 39 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 4.112A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL C 199 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR C 205 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN C 197 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG C 207 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER C 195 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER C 209 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU C 193 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER C 211 " --> pdb=" O HIS C 191 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N HIS C 191 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG C 213 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.246A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.036A pdb=" N ASP D 101 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ALA D 135 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS D 103 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB3, 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: 3.635A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.232A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.818A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.315A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL E 199 " --> pdb=" O GLY E 203 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR E 205 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN E 197 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG E 207 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER E 195 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER E 209 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU E 193 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER E 211 " --> pdb=" O HIS E 191 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS E 191 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG E 213 " --> pdb=" O VAL E 189 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2331 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: 2.45 Time building geometry restraints manager: 1.81 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: 4324 1.34 - 1.46: 3000 1.46 - 1.57: 7303 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14767 Sorted by residual: 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 2.63e+00 bond pdb=" C1 MAN c 5 " pdb=" O5 MAN c 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.53e+00 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 2.50e+00 bond pdb=" C1 MAN c 4 " pdb=" O5 MAN c 4 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.45e+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 2.34e+00 ... (remaining 14762 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 19300 1.13 - 2.27: 551 2.27 - 3.40: 205 3.40 - 4.53: 32 4.53 - 5.66: 16 Bond angle restraints: 20104 Sorted by residual: angle pdb=" N ILE D 429 " pdb=" CA ILE D 429 " pdb=" C ILE D 429 " ideal model delta sigma weight residual 111.81 109.63 2.18 8.60e-01 1.35e+00 6.45e+00 angle pdb=" C TYR D 66 " pdb=" N TRP D 67 " pdb=" CA TRP D 67 " ideal model delta sigma weight residual 121.87 118.29 3.58 1.64e+00 3.72e-01 4.76e+00 angle pdb=" C TYR C 66 " pdb=" N TRP C 67 " pdb=" CA TRP C 67 " ideal model delta sigma weight residual 122.53 119.09 3.44 1.61e+00 3.86e-01 4.57e+00 angle pdb=" CA PRO C 273 " pdb=" C PRO C 273 " pdb=" N LYS C 274 " ideal model delta sigma weight residual 115.12 117.57 -2.45 1.25e+00 6.40e-01 3.84e+00 angle pdb=" CA ATYR E 66 " pdb=" CB ATYR E 66 " pdb=" CG ATYR E 66 " ideal model delta sigma weight residual 113.90 117.37 -3.47 1.80e+00 3.09e-01 3.71e+00 ... (remaining 20099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 8845 21.17 - 42.35: 240 42.35 - 63.52: 26 63.52 - 84.70: 35 84.70 - 105.87: 22 Dihedral angle restraints: 9168 sinusoidal: 4155 harmonic: 5013 Sorted by residual: 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 -177.16 105.87 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" O4 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.93 105.64 1 3.00e+01 1.11e-03 1.35e+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 -176.63 105.34 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 9165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2028 0.059 - 0.117: 297 0.117 - 0.176: 27 0.176 - 0.235: 8 0.235 - 0.294: 5 Chirality restraints: 2365 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 80 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C5 BMA e 3 " pdb=" C4 BMA e 3 " pdb=" C6 BMA e 3 " pdb=" O5 BMA e 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2362 not shown) Planarity restraints: 2460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 254 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.22e+00 pdb=" C GLY A 254 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY A 254 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE A 255 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 257 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C THR A 257 " 0.029 2.00e-02 2.50e+03 pdb=" O THR A 257 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 258 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 256 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C THR A 256 " -0.029 2.00e-02 2.50e+03 pdb=" O THR A 256 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 257 " 0.010 2.00e-02 2.50e+03 ... (remaining 2457 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1050 2.74 - 3.28: 14097 3.28 - 3.82: 24258 3.82 - 4.36: 28797 4.36 - 4.90: 49684 Nonbonded interactions: 117886 Sorted by model distance: nonbonded pdb=" OH TYR C 284 " pdb=" OD1 ASN C 439 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR B 284 " pdb=" OD1 ASN B 439 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR B 202 " pdb=" OH TYR B 205 " model vdw 2.265 3.040 nonbonded pdb=" O PHE A 221 " pdb=" OG1 THR A 225 " model vdw 2.268 3.040 nonbonded pdb=" O THR C 233 " pdb=" OG SER C 236 " model vdw 2.280 3.040 ... (remaining 117881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 65 or resid 67 through 447)) selection = (chain 'B' and (resid 4 through 65 or resid 67 through 447)) selection = (chain 'C' and (resid 4 through 65 or resid 67 through 447)) selection = (chain 'D' and (resid 4 through 65 or resid 67 through 447)) selection = (chain 'E' and (resid 4 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.100 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 0.032 14812 Z= 0.172 Angle : 0.543 5.665 20234 Z= 0.254 Chirality : 0.045 0.294 2365 Planarity : 0.003 0.032 2445 Dihedral : 12.381 105.874 5943 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.19 % Allowed : 3.84 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 2.11 (0.22), residues: 1680 helix: 2.71 (0.21), residues: 618 sheet: 0.54 (0.26), residues: 409 loop : 0.83 (0.29), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 312 TYR 0.014 0.001 TYR B 66 PHE 0.009 0.001 PHE A 212 TRP 0.010 0.001 TRP D 67 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00355 (14767) covalent geometry : angle 0.53502 (20104) SS BOND : bond 0.00121 ( 5) SS BOND : angle 0.43242 ( 10) hydrogen bonds : bond 0.12291 ( 733) hydrogen bonds : angle 4.98824 ( 2331) link_ALPHA1-3 : bond 0.00243 ( 5) link_ALPHA1-3 : angle 1.12439 ( 15) link_ALPHA1-6 : bond 0.00302 ( 5) link_ALPHA1-6 : angle 1.03068 ( 15) link_BETA1-4 : bond 0.00338 ( 15) link_BETA1-4 : angle 1.57873 ( 45) link_NAG-ASN : bond 0.00170 ( 15) link_NAG-ASN : angle 1.25355 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 467 time to evaluate : 0.475 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: symmetry clash REVERT: A 17 ASP cc_start: 0.8942 (m-30) cc_final: 0.8634 (m-30) REVERT: A 215 LYS cc_start: 0.8833 (tttt) cc_final: 0.8523 (mtpp) REVERT: A 231 LEU cc_start: 0.9167 (mt) cc_final: 0.8883 (mp) REVERT: A 237 TRP cc_start: 0.8565 (m-10) cc_final: 0.8228 (m-10) REVERT: A 275 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7812 (pp) REVERT: B 180 ARG cc_start: 0.8631 (mtm110) cc_final: 0.8385 (mtm110) REVERT: B 274 LYS cc_start: 0.8744 (mttt) cc_final: 0.8503 (mttm) REVERT: C 163 ASP cc_start: 0.8487 (m-30) cc_final: 0.8056 (m-30) REVERT: C 239 SER cc_start: 0.9077 (m) cc_final: 0.8865 (t) REVERT: C 283 MET cc_start: 0.8510 (ttm) cc_final: 0.8077 (ttp) REVERT: C 293 PHE cc_start: 0.8685 (t80) cc_final: 0.8235 (t80) REVERT: C 433 PHE cc_start: 0.8511 (t80) cc_final: 0.8174 (t80) REVERT: D 13 LYS cc_start: 0.9192 (tttt) cc_final: 0.8859 (tttt) REVERT: D 18 LYS cc_start: 0.9206 (tttt) cc_final: 0.8947 (tttm) REVERT: D 90 GLN cc_start: 0.9134 (mp10) cc_final: 0.8796 (mp10) REVERT: D 141 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7675 (ttm-80) REVERT: E 9 MET cc_start: 0.7515 (mtp) cc_final: 0.7238 (ttm) REVERT: E 13 LYS cc_start: 0.9085 (tttt) cc_final: 0.8811 (ttpp) REVERT: E 148 GLN cc_start: 0.7314 (mm-40) cc_final: 0.6838 (mm110) REVERT: E 237 TRP cc_start: 0.7990 (m-10) cc_final: 0.7639 (m-10) REVERT: E 278 VAL cc_start: 0.8281 (t) cc_final: 0.8039 (p) REVERT: E 425 ARG cc_start: 0.7384 (mmm-85) cc_final: 0.7017 (mmm-85) REVERT: E 426 TRP cc_start: 0.8369 (m100) cc_final: 0.7786 (m-10) outliers start: 18 outliers final: 7 residues processed: 480 average time/residue: 0.1353 time to fit residues: 91.1009 Evaluate side-chains 350 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 342 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 218 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0170 overall best weight: 2.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 267 HIS A 303 ASN A 309 GLN C 90 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN C 309 GLN E 41 ASN E 309 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.107459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081326 restraints weight = 53981.081| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 4.69 r_work: 0.2918 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14812 Z= 0.204 Angle : 0.645 9.057 20234 Z= 0.323 Chirality : 0.047 0.350 2365 Planarity : 0.005 0.060 2445 Dihedral : 11.270 83.575 2750 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.18 % Allowed : 11.46 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.88 (0.22), residues: 1680 helix: 2.43 (0.20), residues: 621 sheet: 0.49 (0.25), residues: 414 loop : 0.74 (0.28), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 269 TYR 0.026 0.002 TYR E 299 PHE 0.017 0.002 PHE E 221 TRP 0.028 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00467 (14767) covalent geometry : angle 0.63383 (20104) SS BOND : bond 0.00138 ( 5) SS BOND : angle 0.30923 ( 10) hydrogen bonds : bond 0.03902 ( 733) hydrogen bonds : angle 4.29713 ( 2331) link_ALPHA1-3 : bond 0.00906 ( 5) link_ALPHA1-3 : angle 1.99456 ( 15) link_ALPHA1-6 : bond 0.00331 ( 5) link_ALPHA1-6 : angle 2.10327 ( 15) link_BETA1-4 : bond 0.00283 ( 15) link_BETA1-4 : angle 1.67103 ( 45) link_NAG-ASN : bond 0.00216 ( 15) link_NAG-ASN : angle 1.40713 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 356 time to evaluate : 0.540 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 17 ASP cc_start: 0.9197 (m-30) cc_final: 0.8779 (m-30) REVERT: A 52 GLU cc_start: 0.8577 (mp0) cc_final: 0.8372 (mp0) REVERT: A 215 LYS cc_start: 0.8609 (tttt) cc_final: 0.8268 (mtpp) REVERT: A 231 LEU cc_start: 0.9540 (mt) cc_final: 0.9214 (mp) REVERT: A 275 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7788 (pp) REVERT: B 55 MET cc_start: 0.9434 (mmm) cc_final: 0.9162 (mmm) REVERT: B 165 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8267 (mt-10) REVERT: B 274 LYS cc_start: 0.8917 (mttt) cc_final: 0.8461 (mttm) REVERT: C 190 GLU cc_start: 0.8299 (tt0) cc_final: 0.7984 (tt0) REVERT: C 283 MET cc_start: 0.8673 (ttm) cc_final: 0.8073 (ttp) REVERT: C 293 PHE cc_start: 0.8893 (t80) cc_final: 0.8474 (t80) REVERT: D 18 LYS cc_start: 0.9263 (tttt) cc_final: 0.8899 (tttm) REVERT: D 52 GLU cc_start: 0.8817 (mp0) cc_final: 0.8611 (mp0) REVERT: D 90 GLN cc_start: 0.8856 (mp10) cc_final: 0.8425 (mp10) REVERT: D 141 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7921 (ttm-80) REVERT: D 190 GLU cc_start: 0.8649 (tt0) cc_final: 0.8407 (tt0) REVERT: D 261 MET cc_start: 0.8294 (tpt) cc_final: 0.7891 (tpp) REVERT: D 446 TYR cc_start: 0.6502 (m-80) cc_final: 0.6147 (m-10) REVERT: E 9 MET cc_start: 0.7302 (mtp) cc_final: 0.7085 (ttm) REVERT: E 14 GLU cc_start: 0.9229 (pt0) cc_final: 0.8905 (pp20) REVERT: E 21 LYS cc_start: 0.9202 (mmmt) cc_final: 0.8678 (mmmt) REVERT: E 40 MET cc_start: 0.8892 (mtt) cc_final: 0.8462 (mtt) REVERT: E 117 ARG cc_start: 0.8713 (ttm170) cc_final: 0.8214 (ttm-80) REVERT: E 148 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6890 (mm110) REVERT: E 180 ARG cc_start: 0.8375 (mtm110) cc_final: 0.7730 (ptp90) REVERT: E 237 TRP cc_start: 0.8786 (m-10) cc_final: 0.8408 (m-90) REVERT: E 425 ARG cc_start: 0.7580 (mmm-85) cc_final: 0.7082 (mmm-85) REVERT: E 426 TRP cc_start: 0.8518 (m100) cc_final: 0.7894 (m-10) outliers start: 48 outliers final: 35 residues processed: 381 average time/residue: 0.1323 time to fit residues: 71.7963 Evaluate side-chains 372 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 336 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 437 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 136 optimal weight: 0.0370 chunk 1 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 155 optimal weight: 0.0370 chunk 135 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 148 GLN B 185 GLN B 439 ASN C 267 HIS D 41 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.113402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088013 restraints weight = 45869.018| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 4.25 r_work: 0.3040 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14812 Z= 0.120 Angle : 0.599 10.692 20234 Z= 0.299 Chirality : 0.046 0.260 2365 Planarity : 0.004 0.038 2445 Dihedral : 10.369 76.886 2750 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.72 % Allowed : 13.11 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.75 (0.22), residues: 1680 helix: 2.21 (0.20), residues: 621 sheet: 0.67 (0.26), residues: 394 loop : 0.58 (0.28), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 180 TYR 0.042 0.001 TYR C 299 PHE 0.020 0.001 PHE A 212 TRP 0.048 0.001 TRP C 237 HIS 0.007 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00266 (14767) covalent geometry : angle 0.58993 (20104) SS BOND : bond 0.00125 ( 5) SS BOND : angle 0.29796 ( 10) hydrogen bonds : bond 0.03597 ( 733) hydrogen bonds : angle 4.10028 ( 2331) link_ALPHA1-3 : bond 0.01086 ( 5) link_ALPHA1-3 : angle 1.71006 ( 15) link_ALPHA1-6 : bond 0.00699 ( 5) link_ALPHA1-6 : angle 2.00463 ( 15) link_BETA1-4 : bond 0.00316 ( 15) link_BETA1-4 : angle 1.48970 ( 45) link_NAG-ASN : bond 0.00262 ( 15) link_NAG-ASN : angle 1.24137 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 354 time to evaluate : 0.555 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9223 (m-30) cc_final: 0.8791 (m-30) REVERT: A 215 LYS cc_start: 0.8534 (tttt) cc_final: 0.8306 (mtpp) REVERT: A 231 LEU cc_start: 0.9508 (mt) cc_final: 0.9212 (mp) REVERT: A 264 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8381 (tp) REVERT: A 275 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7758 (pp) REVERT: A 306 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8406 (t80) REVERT: B 55 MET cc_start: 0.9367 (mmm) cc_final: 0.9162 (mmm) REVERT: B 95 ASP cc_start: 0.8416 (p0) cc_final: 0.8175 (p0) REVERT: B 165 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8292 (mt-10) REVERT: B 182 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6865 (mm-30) REVERT: B 224 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7074 (mm-40) REVERT: C 55 MET cc_start: 0.8446 (mtm) cc_final: 0.8243 (mtp) REVERT: C 163 ASP cc_start: 0.8905 (m-30) cc_final: 0.8317 (m-30) REVERT: C 190 GLU cc_start: 0.8369 (tt0) cc_final: 0.8001 (tt0) REVERT: C 240 PHE cc_start: 0.8141 (m-80) cc_final: 0.7731 (m-80) REVERT: C 266 THR cc_start: 0.8388 (p) cc_final: 0.8044 (t) REVERT: C 283 MET cc_start: 0.8628 (ttm) cc_final: 0.7937 (ttp) REVERT: C 293 PHE cc_start: 0.8812 (t80) cc_final: 0.8390 (t80) REVERT: C 299 TYR cc_start: 0.9142 (t80) cc_final: 0.8762 (t80) REVERT: D 18 LYS cc_start: 0.9262 (tttt) cc_final: 0.8889 (tttm) REVERT: D 52 GLU cc_start: 0.8757 (mp0) cc_final: 0.8472 (mp0) REVERT: D 90 GLN cc_start: 0.8861 (mp10) cc_final: 0.8415 (mp10) REVERT: D 192 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8193 (ttm110) REVERT: D 200 PHE cc_start: 0.8407 (m-80) cc_final: 0.8189 (m-10) REVERT: E 9 MET cc_start: 0.7292 (mtp) cc_final: 0.7043 (ttm) REVERT: E 21 LYS cc_start: 0.9247 (mmmt) cc_final: 0.8812 (mmmt) REVERT: E 40 MET cc_start: 0.8869 (mtt) cc_final: 0.8407 (mtt) REVERT: E 55 MET cc_start: 0.8629 (mmm) cc_final: 0.8076 (mmm) REVERT: E 112 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8104 (ttpp) REVERT: E 117 ARG cc_start: 0.8623 (ttm170) cc_final: 0.8073 (ttm-80) REVERT: E 148 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6786 (mm110) REVERT: E 153 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8552 (mm-30) REVERT: E 237 TRP cc_start: 0.8693 (m-10) cc_final: 0.8345 (m-90) REVERT: E 286 MET cc_start: 0.8435 (tpt) cc_final: 0.8154 (tpp) REVERT: E 425 ARG cc_start: 0.7531 (mmm-85) cc_final: 0.7038 (mmm-85) REVERT: E 426 TRP cc_start: 0.8460 (m100) cc_final: 0.7824 (m-10) outliers start: 41 outliers final: 26 residues processed: 377 average time/residue: 0.1376 time to fit residues: 73.7253 Evaluate side-chains 368 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 337 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain E residue 437 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN E 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.108969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082406 restraints weight = 63278.781| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 5.04 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14812 Z= 0.145 Angle : 0.613 11.077 20234 Z= 0.304 Chirality : 0.047 0.307 2365 Planarity : 0.004 0.049 2445 Dihedral : 9.818 73.638 2749 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.84 % Allowed : 13.05 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.65 (0.22), residues: 1680 helix: 2.14 (0.21), residues: 621 sheet: 0.66 (0.26), residues: 399 loop : 0.50 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 180 TYR 0.027 0.001 TYR C 299 PHE 0.021 0.001 PHE A 212 TRP 0.066 0.002 TRP C 237 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00330 (14767) covalent geometry : angle 0.60358 (20104) SS BOND : bond 0.00082 ( 5) SS BOND : angle 0.27741 ( 10) hydrogen bonds : bond 0.03482 ( 733) hydrogen bonds : angle 4.05682 ( 2331) link_ALPHA1-3 : bond 0.01080 ( 5) link_ALPHA1-3 : angle 1.87754 ( 15) link_ALPHA1-6 : bond 0.00699 ( 5) link_ALPHA1-6 : angle 2.07012 ( 15) link_BETA1-4 : bond 0.00298 ( 15) link_BETA1-4 : angle 1.46110 ( 45) link_NAG-ASN : bond 0.00199 ( 15) link_NAG-ASN : angle 1.29665 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 336 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9132 (m-30) cc_final: 0.8691 (m-30) REVERT: A 190 GLU cc_start: 0.8098 (tt0) cc_final: 0.7863 (pt0) REVERT: A 215 LYS cc_start: 0.8304 (tttt) cc_final: 0.8101 (mtpp) REVERT: A 231 LEU cc_start: 0.9499 (mt) cc_final: 0.9222 (mp) REVERT: A 275 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7752 (pp) REVERT: A 306 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8429 (t80) REVERT: B 165 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7656 (mt-10) REVERT: B 182 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6603 (mm-30) REVERT: B 224 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.6866 (mm-40) REVERT: B 274 LYS cc_start: 0.7988 (mttt) cc_final: 0.7756 (mttm) REVERT: C 163 ASP cc_start: 0.8642 (m-30) cc_final: 0.8025 (m-30) REVERT: C 190 GLU cc_start: 0.7881 (tt0) cc_final: 0.7450 (tt0) REVERT: C 240 PHE cc_start: 0.8033 (m-80) cc_final: 0.7641 (m-80) REVERT: C 283 MET cc_start: 0.8422 (ttm) cc_final: 0.7672 (ttp) REVERT: C 293 PHE cc_start: 0.8520 (t80) cc_final: 0.8107 (t80) REVERT: D 18 LYS cc_start: 0.9244 (tttt) cc_final: 0.8875 (tttm) REVERT: D 52 GLU cc_start: 0.8653 (mp0) cc_final: 0.8345 (mp0) REVERT: D 90 GLN cc_start: 0.8639 (mp10) cc_final: 0.8188 (mp10) REVERT: D 192 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7686 (ttm110) REVERT: D 200 PHE cc_start: 0.8453 (m-80) cc_final: 0.8210 (m-10) REVERT: E 21 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8760 (mmmt) REVERT: E 40 MET cc_start: 0.8187 (mtt) cc_final: 0.7668 (mtt) REVERT: E 55 MET cc_start: 0.8329 (mmm) cc_final: 0.8099 (mmm) REVERT: E 117 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7559 (ttm-80) REVERT: E 138 MET cc_start: 0.8807 (mtm) cc_final: 0.8277 (mtp) REVERT: E 148 GLN cc_start: 0.7142 (mm-40) cc_final: 0.6510 (mm110) REVERT: E 153 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8145 (mm-30) REVERT: E 180 ARG cc_start: 0.8276 (mtm110) cc_final: 0.7856 (ttp-110) REVERT: E 237 TRP cc_start: 0.8798 (m-10) cc_final: 0.8362 (m-90) REVERT: E 425 ARG cc_start: 0.7528 (mmm-85) cc_final: 0.7036 (mmm-85) REVERT: E 426 TRP cc_start: 0.8398 (m100) cc_final: 0.7757 (m-10) outliers start: 58 outliers final: 43 residues processed: 367 average time/residue: 0.1357 time to fit residues: 70.9219 Evaluate side-chains 371 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 324 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 437 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.109022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083952 restraints weight = 41947.000| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.07 r_work: 0.2967 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14812 Z= 0.147 Angle : 0.629 12.821 20234 Z= 0.309 Chirality : 0.047 0.384 2365 Planarity : 0.004 0.037 2445 Dihedral : 9.368 69.655 2748 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.84 % Allowed : 13.51 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.61 (0.22), residues: 1680 helix: 2.12 (0.21), residues: 621 sheet: 0.64 (0.26), residues: 399 loop : 0.45 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 180 TYR 0.040 0.002 TYR C 299 PHE 0.021 0.001 PHE A 212 TRP 0.067 0.001 TRP C 237 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00336 (14767) covalent geometry : angle 0.61968 (20104) SS BOND : bond 0.00087 ( 5) SS BOND : angle 0.23041 ( 10) hydrogen bonds : bond 0.03431 ( 733) hydrogen bonds : angle 4.00154 ( 2331) link_ALPHA1-3 : bond 0.01120 ( 5) link_ALPHA1-3 : angle 1.93066 ( 15) link_ALPHA1-6 : bond 0.00771 ( 5) link_ALPHA1-6 : angle 2.09168 ( 15) link_BETA1-4 : bond 0.00301 ( 15) link_BETA1-4 : angle 1.42999 ( 45) link_NAG-ASN : bond 0.00176 ( 15) link_NAG-ASN : angle 1.30604 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 335 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9196 (m-30) cc_final: 0.8803 (m-30) REVERT: A 52 GLU cc_start: 0.8375 (mp0) cc_final: 0.8065 (mp0) REVERT: A 55 MET cc_start: 0.8854 (mmm) cc_final: 0.7710 (mmm) REVERT: A 190 GLU cc_start: 0.8785 (tt0) cc_final: 0.8515 (pt0) REVERT: A 215 LYS cc_start: 0.8502 (tttt) cc_final: 0.8267 (mtpp) REVERT: A 231 LEU cc_start: 0.9547 (mt) cc_final: 0.9262 (mp) REVERT: A 306 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8446 (t80) REVERT: B 55 MET cc_start: 0.9396 (mmm) cc_final: 0.9142 (mmm) REVERT: B 103 LYS cc_start: 0.9179 (tptt) cc_final: 0.8897 (tptp) REVERT: B 165 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8371 (mt-10) REVERT: B 182 GLU cc_start: 0.7216 (mm-30) cc_final: 0.7000 (mm-30) REVERT: B 224 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7153 (mm-40) REVERT: B 274 LYS cc_start: 0.8012 (mttt) cc_final: 0.7754 (mttm) REVERT: C 9 MET cc_start: 0.8225 (mtt) cc_final: 0.7958 (mmt) REVERT: C 163 ASP cc_start: 0.8895 (m-30) cc_final: 0.8310 (m-30) REVERT: C 190 GLU cc_start: 0.8404 (tt0) cc_final: 0.8048 (tt0) REVERT: C 240 PHE cc_start: 0.8035 (m-80) cc_final: 0.7707 (m-80) REVERT: C 283 MET cc_start: 0.8640 (ttm) cc_final: 0.7960 (ttp) REVERT: C 293 PHE cc_start: 0.8836 (t80) cc_final: 0.8410 (t80) REVERT: D 18 LYS cc_start: 0.9255 (tttt) cc_final: 0.8885 (tttm) REVERT: D 52 GLU cc_start: 0.8792 (mp0) cc_final: 0.8466 (mp0) REVERT: D 90 GLN cc_start: 0.8906 (mp10) cc_final: 0.8455 (mp10) REVERT: D 190 GLU cc_start: 0.8703 (tt0) cc_final: 0.8408 (tt0) REVERT: D 192 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8122 (ttm110) REVERT: D 223 LEU cc_start: 0.9170 (tp) cc_final: 0.8896 (tt) REVERT: E 40 MET cc_start: 0.8828 (mtt) cc_final: 0.8364 (mtt) REVERT: E 55 MET cc_start: 0.8771 (mmm) cc_final: 0.8476 (mmm) REVERT: E 117 ARG cc_start: 0.8572 (ttm170) cc_final: 0.7950 (ttm-80) REVERT: E 138 MET cc_start: 0.8855 (mtm) cc_final: 0.8368 (mtp) REVERT: E 148 GLN cc_start: 0.7478 (mm-40) cc_final: 0.6765 (mm110) REVERT: E 153 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8572 (mm-30) REVERT: E 237 TRP cc_start: 0.8773 (m-10) cc_final: 0.8316 (m-90) REVERT: E 425 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7063 (mmm-85) REVERT: E 426 TRP cc_start: 0.8494 (m100) cc_final: 0.7831 (m-10) outliers start: 58 outliers final: 49 residues processed: 368 average time/residue: 0.1335 time to fit residues: 70.0840 Evaluate side-chains 372 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 320 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 437 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 70 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 0.0370 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 113 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083721 restraints weight = 51890.352| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 4.57 r_work: 0.2956 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14812 Z= 0.131 Angle : 0.625 12.345 20234 Z= 0.307 Chirality : 0.047 0.386 2365 Planarity : 0.004 0.055 2445 Dihedral : 8.940 65.403 2746 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.71 % Allowed : 13.97 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.63 (0.22), residues: 1680 helix: 2.11 (0.21), residues: 621 sheet: 0.60 (0.25), residues: 414 loop : 0.53 (0.28), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 180 TYR 0.041 0.002 TYR C 299 PHE 0.022 0.001 PHE A 212 TRP 0.063 0.001 TRP C 237 HIS 0.014 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00298 (14767) covalent geometry : angle 0.61611 (20104) SS BOND : bond 0.00075 ( 5) SS BOND : angle 0.13408 ( 10) hydrogen bonds : bond 0.03371 ( 733) hydrogen bonds : angle 3.97070 ( 2331) link_ALPHA1-3 : bond 0.01140 ( 5) link_ALPHA1-3 : angle 1.95938 ( 15) link_ALPHA1-6 : bond 0.00856 ( 5) link_ALPHA1-6 : angle 2.05766 ( 15) link_BETA1-4 : bond 0.00324 ( 15) link_BETA1-4 : angle 1.39509 ( 45) link_NAG-ASN : bond 0.00203 ( 15) link_NAG-ASN : angle 1.28398 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 335 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9218 (m-30) cc_final: 0.8836 (m-30) REVERT: A 55 MET cc_start: 0.8854 (mmm) cc_final: 0.7816 (mmm) REVERT: A 190 GLU cc_start: 0.8811 (tt0) cc_final: 0.8539 (pt0) REVERT: A 215 LYS cc_start: 0.8487 (tttt) cc_final: 0.8260 (mtpp) REVERT: A 231 LEU cc_start: 0.9525 (mt) cc_final: 0.9237 (mp) REVERT: A 306 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8482 (t80) REVERT: B 103 LYS cc_start: 0.9177 (tptt) cc_final: 0.8890 (tptp) REVERT: B 165 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8434 (mt-10) REVERT: B 182 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6980 (mm-30) REVERT: B 185 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8396 (mp10) REVERT: B 224 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7163 (mm-40) REVERT: B 274 LYS cc_start: 0.8035 (mttt) cc_final: 0.7511 (mttm) REVERT: C 9 MET cc_start: 0.8203 (mtt) cc_final: 0.7952 (mmt) REVERT: C 163 ASP cc_start: 0.8915 (m-30) cc_final: 0.8333 (m-30) REVERT: C 190 GLU cc_start: 0.8425 (tt0) cc_final: 0.8102 (tt0) REVERT: C 240 PHE cc_start: 0.7934 (m-80) cc_final: 0.7598 (m-80) REVERT: C 250 ARG cc_start: 0.8156 (mtp180) cc_final: 0.7935 (mtt180) REVERT: C 283 MET cc_start: 0.8629 (ttm) cc_final: 0.7945 (ttp) REVERT: C 293 PHE cc_start: 0.8830 (t80) cc_final: 0.8416 (t80) REVERT: D 18 LYS cc_start: 0.9263 (tttt) cc_final: 0.8893 (tttm) REVERT: D 52 GLU cc_start: 0.8833 (mp0) cc_final: 0.8479 (mp0) REVERT: D 90 GLN cc_start: 0.8905 (mp10) cc_final: 0.8447 (mp10) REVERT: D 190 GLU cc_start: 0.8769 (tt0) cc_final: 0.8534 (tt0) REVERT: D 192 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8137 (ttm110) REVERT: D 446 TYR cc_start: 0.5929 (m-10) cc_final: 0.5630 (m-10) REVERT: E 40 MET cc_start: 0.8834 (mtt) cc_final: 0.8378 (mtt) REVERT: E 138 MET cc_start: 0.8817 (mtm) cc_final: 0.8528 (mtp) REVERT: E 148 GLN cc_start: 0.7553 (mm-40) cc_final: 0.6827 (mm110) REVERT: E 153 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8588 (mm-30) REVERT: E 180 ARG cc_start: 0.8323 (mtm110) cc_final: 0.8069 (ttp-110) REVERT: E 229 SER cc_start: 0.8891 (m) cc_final: 0.8502 (p) REVERT: E 237 TRP cc_start: 0.8810 (m-10) cc_final: 0.8267 (m-90) REVERT: E 269 ARG cc_start: 0.7862 (tpt90) cc_final: 0.7309 (mmm160) REVERT: E 425 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.7026 (mmm-85) REVERT: E 426 TRP cc_start: 0.8474 (m100) cc_final: 0.7808 (m-10) outliers start: 56 outliers final: 44 residues processed: 367 average time/residue: 0.1390 time to fit residues: 72.3906 Evaluate side-chains 367 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 437 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 265 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.082441 restraints weight = 51863.739| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 4.57 r_work: 0.2930 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14812 Z= 0.179 Angle : 0.668 14.059 20234 Z= 0.324 Chirality : 0.047 0.302 2365 Planarity : 0.004 0.044 2445 Dihedral : 8.745 63.031 2746 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.84 % Allowed : 14.24 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.62 (0.22), residues: 1680 helix: 2.12 (0.21), residues: 621 sheet: 0.56 (0.25), residues: 414 loop : 0.52 (0.28), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 180 TYR 0.040 0.002 TYR C 299 PHE 0.022 0.002 PHE A 212 TRP 0.057 0.001 TRP C 237 HIS 0.011 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00413 (14767) covalent geometry : angle 0.65883 (20104) SS BOND : bond 0.00085 ( 5) SS BOND : angle 0.25226 ( 10) hydrogen bonds : bond 0.03404 ( 733) hydrogen bonds : angle 4.00085 ( 2331) link_ALPHA1-3 : bond 0.01073 ( 5) link_ALPHA1-3 : angle 1.97700 ( 15) link_ALPHA1-6 : bond 0.00832 ( 5) link_ALPHA1-6 : angle 2.06415 ( 15) link_BETA1-4 : bond 0.00312 ( 15) link_BETA1-4 : angle 1.44264 ( 45) link_NAG-ASN : bond 0.00166 ( 15) link_NAG-ASN : angle 1.36078 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 317 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9222 (m-30) cc_final: 0.8830 (m-30) REVERT: A 55 MET cc_start: 0.8874 (mmm) cc_final: 0.7793 (mmm) REVERT: A 190 GLU cc_start: 0.8843 (tt0) cc_final: 0.8550 (pt0) REVERT: A 215 LYS cc_start: 0.8521 (tttt) cc_final: 0.8289 (mtpp) REVERT: A 306 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8498 (t80) REVERT: B 68 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7899 (tpp80) REVERT: B 103 LYS cc_start: 0.9190 (tptt) cc_final: 0.8899 (tptp) REVERT: B 165 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8476 (mt-10) REVERT: B 185 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8363 (mp10) REVERT: B 224 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7191 (mm-40) REVERT: C 9 MET cc_start: 0.8222 (mtt) cc_final: 0.7984 (mmt) REVERT: C 163 ASP cc_start: 0.8908 (m-30) cc_final: 0.8332 (m-30) REVERT: C 190 GLU cc_start: 0.8458 (tt0) cc_final: 0.8126 (tt0) REVERT: C 240 PHE cc_start: 0.8017 (m-80) cc_final: 0.7718 (m-80) REVERT: C 283 MET cc_start: 0.8595 (ttm) cc_final: 0.7907 (ttp) REVERT: C 293 PHE cc_start: 0.8842 (t80) cc_final: 0.8422 (t80) REVERT: D 18 LYS cc_start: 0.9268 (tttt) cc_final: 0.8900 (tttm) REVERT: D 52 GLU cc_start: 0.8855 (mp0) cc_final: 0.8494 (mp0) REVERT: D 90 GLN cc_start: 0.8919 (mp10) cc_final: 0.8462 (mp10) REVERT: D 190 GLU cc_start: 0.8767 (tt0) cc_final: 0.8548 (tt0) REVERT: D 192 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8110 (ttm110) REVERT: D 446 TYR cc_start: 0.6027 (m-10) cc_final: 0.5764 (m-10) REVERT: E 40 MET cc_start: 0.8858 (mtt) cc_final: 0.8413 (mtt) REVERT: E 148 GLN cc_start: 0.7492 (mm-40) cc_final: 0.6627 (mm110) REVERT: E 180 ARG cc_start: 0.8369 (mtm110) cc_final: 0.7873 (ttp-110) REVERT: E 229 SER cc_start: 0.8919 (m) cc_final: 0.8532 (p) REVERT: E 237 TRP cc_start: 0.8781 (m-10) cc_final: 0.8227 (m-90) REVERT: E 425 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.7045 (mmm-85) REVERT: E 426 TRP cc_start: 0.8506 (m100) cc_final: 0.7830 (m-10) outliers start: 58 outliers final: 50 residues processed: 350 average time/residue: 0.1331 time to fit residues: 67.0024 Evaluate side-chains 364 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 310 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 437 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 67 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 93 optimal weight: 0.0370 chunk 123 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 265 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.083245 restraints weight = 57354.416| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.83 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14812 Z= 0.132 Angle : 0.645 12.538 20234 Z= 0.314 Chirality : 0.047 0.410 2365 Planarity : 0.004 0.041 2445 Dihedral : 8.344 60.568 2746 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.51 % Allowed : 14.44 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.66 (0.22), residues: 1680 helix: 2.12 (0.21), residues: 621 sheet: 0.56 (0.25), residues: 438 loop : 0.61 (0.29), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 180 TYR 0.039 0.001 TYR C 299 PHE 0.021 0.001 PHE A 212 TRP 0.045 0.001 TRP C 237 HIS 0.011 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00299 (14767) covalent geometry : angle 0.63632 (20104) SS BOND : bond 0.00065 ( 5) SS BOND : angle 0.21286 ( 10) hydrogen bonds : bond 0.03387 ( 733) hydrogen bonds : angle 3.94720 ( 2331) link_ALPHA1-3 : bond 0.01080 ( 5) link_ALPHA1-3 : angle 1.94893 ( 15) link_ALPHA1-6 : bond 0.00944 ( 5) link_ALPHA1-6 : angle 1.99763 ( 15) link_BETA1-4 : bond 0.00344 ( 15) link_BETA1-4 : angle 1.39149 ( 45) link_NAG-ASN : bond 0.00194 ( 15) link_NAG-ASN : angle 1.28661 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 323 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9130 (m-30) cc_final: 0.8718 (m-30) REVERT: A 52 GLU cc_start: 0.8280 (mp0) cc_final: 0.7957 (mp0) REVERT: A 190 GLU cc_start: 0.8243 (tt0) cc_final: 0.7975 (pt0) REVERT: A 215 LYS cc_start: 0.8293 (tttt) cc_final: 0.8074 (mtpp) REVERT: A 306 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8531 (t80) REVERT: B 103 LYS cc_start: 0.9145 (tptt) cc_final: 0.8848 (tptp) REVERT: B 165 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7729 (mt-10) REVERT: B 185 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: B 224 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.6960 (mm-40) REVERT: C 9 MET cc_start: 0.8164 (mtt) cc_final: 0.7918 (mmt) REVERT: C 190 GLU cc_start: 0.8094 (tt0) cc_final: 0.7851 (tm-30) REVERT: C 240 PHE cc_start: 0.7850 (m-80) cc_final: 0.7637 (m-80) REVERT: C 261 MET cc_start: 0.8766 (ttm) cc_final: 0.8493 (ttt) REVERT: D 18 LYS cc_start: 0.9229 (tttt) cc_final: 0.8855 (tttm) REVERT: D 52 GLU cc_start: 0.8632 (mp0) cc_final: 0.8183 (mp0) REVERT: D 90 GLN cc_start: 0.8675 (mp10) cc_final: 0.8196 (mp10) REVERT: D 153 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8211 (mm-30) REVERT: E 21 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8535 (mmtm) REVERT: E 40 MET cc_start: 0.8226 (mtt) cc_final: 0.7693 (mtt) REVERT: E 55 MET cc_start: 0.8104 (mmm) cc_final: 0.7376 (mmm) REVERT: E 148 GLN cc_start: 0.6867 (mm-40) cc_final: 0.6155 (mm110) REVERT: E 180 ARG cc_start: 0.8262 (mtm110) cc_final: 0.7780 (ttp-110) REVERT: E 185 GLN cc_start: 0.8179 (mp10) cc_final: 0.7802 (mp10) REVERT: E 229 SER cc_start: 0.8780 (m) cc_final: 0.8406 (p) REVERT: E 237 TRP cc_start: 0.8716 (m-10) cc_final: 0.8155 (m-90) REVERT: E 425 ARG cc_start: 0.7548 (mmm-85) cc_final: 0.6997 (mmm-85) REVERT: E 426 TRP cc_start: 0.8427 (m100) cc_final: 0.7754 (m-10) outliers start: 53 outliers final: 44 residues processed: 353 average time/residue: 0.1315 time to fit residues: 67.1958 Evaluate side-chains 357 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 310 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 160 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 149 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 265 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.083203 restraints weight = 48869.329| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.44 r_work: 0.2949 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14812 Z= 0.158 Angle : 0.664 14.069 20234 Z= 0.323 Chirality : 0.047 0.330 2365 Planarity : 0.004 0.038 2445 Dihedral : 8.092 58.910 2746 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.51 % Allowed : 14.83 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.62 (0.22), residues: 1680 helix: 2.06 (0.21), residues: 621 sheet: 0.57 (0.25), residues: 433 loop : 0.59 (0.29), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 180 TYR 0.043 0.002 TYR C 299 PHE 0.024 0.001 PHE A 212 TRP 0.042 0.001 TRP C 237 HIS 0.009 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00365 (14767) covalent geometry : angle 0.65499 (20104) SS BOND : bond 0.00051 ( 5) SS BOND : angle 0.25312 ( 10) hydrogen bonds : bond 0.03433 ( 733) hydrogen bonds : angle 3.98789 ( 2331) link_ALPHA1-3 : bond 0.01078 ( 5) link_ALPHA1-3 : angle 1.96161 ( 15) link_ALPHA1-6 : bond 0.00956 ( 5) link_ALPHA1-6 : angle 1.94353 ( 15) link_BETA1-4 : bond 0.00349 ( 15) link_BETA1-4 : angle 1.42422 ( 45) link_NAG-ASN : bond 0.00175 ( 15) link_NAG-ASN : angle 1.35180 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 321 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9217 (m-30) cc_final: 0.8829 (m-30) REVERT: A 55 MET cc_start: 0.8931 (mmm) cc_final: 0.8278 (mmm) REVERT: A 190 GLU cc_start: 0.8813 (tt0) cc_final: 0.8514 (pt0) REVERT: A 215 LYS cc_start: 0.8499 (tttt) cc_final: 0.8268 (mtpp) REVERT: A 306 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8522 (t80) REVERT: B 103 LYS cc_start: 0.9190 (tptt) cc_final: 0.8889 (tptp) REVERT: B 137 MET cc_start: 0.8497 (mmm) cc_final: 0.8271 (mmm) REVERT: B 165 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8444 (mt-10) REVERT: B 185 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8472 (mp10) REVERT: B 224 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7265 (mm-40) REVERT: C 190 GLU cc_start: 0.8501 (tt0) cc_final: 0.8237 (tm-30) REVERT: C 215 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8377 (ptmt) REVERT: C 283 MET cc_start: 0.8942 (ttp) cc_final: 0.8726 (ttm) REVERT: D 18 LYS cc_start: 0.9268 (tttt) cc_final: 0.8898 (tttm) REVERT: D 40 MET cc_start: 0.9151 (mmt) cc_final: 0.8833 (tpp) REVERT: D 52 GLU cc_start: 0.8810 (mp0) cc_final: 0.8402 (mp0) REVERT: D 90 GLN cc_start: 0.8905 (mp10) cc_final: 0.8447 (mp10) REVERT: D 190 GLU cc_start: 0.8831 (tt0) cc_final: 0.8425 (pt0) REVERT: E 40 MET cc_start: 0.8875 (mtt) cc_final: 0.8405 (mtt) REVERT: E 55 MET cc_start: 0.8693 (mmm) cc_final: 0.8194 (mmm) REVERT: E 148 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6376 (mm110) REVERT: E 180 ARG cc_start: 0.8323 (mtm110) cc_final: 0.7818 (ttp-110) REVERT: E 185 GLN cc_start: 0.8493 (mp10) cc_final: 0.8184 (mp10) REVERT: E 229 SER cc_start: 0.8925 (m) cc_final: 0.8540 (p) REVERT: E 237 TRP cc_start: 0.8775 (m-10) cc_final: 0.8193 (m-90) REVERT: E 286 MET cc_start: 0.8368 (tpt) cc_final: 0.8153 (tpp) REVERT: E 425 ARG cc_start: 0.7497 (mmm-85) cc_final: 0.6997 (mmm-85) REVERT: E 426 TRP cc_start: 0.8523 (m100) cc_final: 0.7847 (m-10) outliers start: 53 outliers final: 48 residues processed: 349 average time/residue: 0.1290 time to fit residues: 65.2166 Evaluate side-chains 359 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 308 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 437 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 25 optimal weight: 9.9990 chunk 57 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 0.0000 chunk 142 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 overall best weight: 0.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 265 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.083769 restraints weight = 61879.652| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 5.03 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14812 Z= 0.120 Angle : 0.659 13.912 20234 Z= 0.319 Chirality : 0.048 0.424 2365 Planarity : 0.004 0.038 2445 Dihedral : 7.688 58.659 2746 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.85 % Allowed : 15.83 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.64 (0.22), residues: 1680 helix: 2.03 (0.21), residues: 621 sheet: 0.63 (0.25), residues: 433 loop : 0.62 (0.29), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 180 TYR 0.039 0.001 TYR C 299 PHE 0.022 0.001 PHE A 212 TRP 0.038 0.001 TRP C 237 HIS 0.010 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00266 (14767) covalent geometry : angle 0.65146 (20104) SS BOND : bond 0.00061 ( 5) SS BOND : angle 0.24543 ( 10) hydrogen bonds : bond 0.03333 ( 733) hydrogen bonds : angle 3.90779 ( 2331) link_ALPHA1-3 : bond 0.01085 ( 5) link_ALPHA1-3 : angle 1.89296 ( 15) link_ALPHA1-6 : bond 0.01060 ( 5) link_ALPHA1-6 : angle 1.87020 ( 15) link_BETA1-4 : bond 0.00403 ( 15) link_BETA1-4 : angle 1.34815 ( 45) link_NAG-ASN : bond 0.00234 ( 15) link_NAG-ASN : angle 1.26572 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 321 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9141 (m-30) cc_final: 0.8753 (m-30) REVERT: A 52 GLU cc_start: 0.8283 (mp0) cc_final: 0.7973 (mp0) REVERT: A 55 MET cc_start: 0.8953 (mmm) cc_final: 0.8292 (mmm) REVERT: A 190 GLU cc_start: 0.8208 (tt0) cc_final: 0.8004 (pt0) REVERT: A 306 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8510 (t80) REVERT: B 18 LYS cc_start: 0.9231 (tmtt) cc_final: 0.8941 (tppt) REVERT: B 103 LYS cc_start: 0.9151 (tptt) cc_final: 0.8842 (tptp) REVERT: B 165 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7729 (mt-10) REVERT: B 185 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8296 (mp10) REVERT: B 224 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.6960 (mm-40) REVERT: B 277 TYR cc_start: 0.7337 (p90) cc_final: 0.7037 (p90) REVERT: C 190 GLU cc_start: 0.8138 (tt0) cc_final: 0.7930 (tm-30) REVERT: C 283 MET cc_start: 0.8719 (ttp) cc_final: 0.8454 (ttm) REVERT: D 18 LYS cc_start: 0.9227 (tttt) cc_final: 0.8855 (tttm) REVERT: D 40 MET cc_start: 0.8777 (mmt) cc_final: 0.8448 (tpp) REVERT: D 52 GLU cc_start: 0.8594 (mp0) cc_final: 0.8095 (mp0) REVERT: D 55 MET cc_start: 0.8937 (mmm) cc_final: 0.8542 (mmm) REVERT: D 90 GLN cc_start: 0.8690 (mp10) cc_final: 0.8239 (mp10) REVERT: D 99 LEU cc_start: 0.9177 (tt) cc_final: 0.8940 (tp) REVERT: D 153 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8247 (mm-30) REVERT: D 190 GLU cc_start: 0.8463 (tt0) cc_final: 0.8044 (pt0) REVERT: E 21 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8500 (mmtm) REVERT: E 40 MET cc_start: 0.8210 (mtt) cc_final: 0.7679 (mtt) REVERT: E 55 MET cc_start: 0.8298 (mmm) cc_final: 0.7806 (mmm) REVERT: E 148 GLN cc_start: 0.6643 (mm-40) cc_final: 0.5901 (mm110) REVERT: E 153 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8068 (mm-30) REVERT: E 180 ARG cc_start: 0.8242 (mtm110) cc_final: 0.7774 (ttp-110) REVERT: E 185 GLN cc_start: 0.8203 (mp10) cc_final: 0.7883 (mp10) REVERT: E 229 SER cc_start: 0.8758 (m) cc_final: 0.8402 (p) REVERT: E 237 TRP cc_start: 0.8754 (m-10) cc_final: 0.8199 (m-90) REVERT: E 269 ARG cc_start: 0.7973 (tpt90) cc_final: 0.7622 (tpm170) REVERT: E 425 ARG cc_start: 0.7448 (mmm-85) cc_final: 0.6946 (mmm-85) REVERT: E 426 TRP cc_start: 0.8428 (m100) cc_final: 0.7755 (m-10) outliers start: 43 outliers final: 40 residues processed: 345 average time/residue: 0.1254 time to fit residues: 63.2041 Evaluate side-chains 349 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 306 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 265 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.084283 restraints weight = 56471.307| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.81 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14812 Z= 0.129 Angle : 0.658 13.693 20234 Z= 0.319 Chirality : 0.048 0.357 2365 Planarity : 0.004 0.040 2445 Dihedral : 7.430 58.510 2746 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.98 % Allowed : 15.83 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.68 (0.22), residues: 1680 helix: 2.07 (0.21), residues: 621 sheet: 0.66 (0.25), residues: 433 loop : 0.63 (0.29), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 250 TYR 0.039 0.001 TYR C 299 PHE 0.037 0.001 PHE E 293 TRP 0.064 0.002 TRP B 237 HIS 0.009 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00295 (14767) covalent geometry : angle 0.65051 (20104) SS BOND : bond 0.00053 ( 5) SS BOND : angle 0.20705 ( 10) hydrogen bonds : bond 0.03323 ( 733) hydrogen bonds : angle 3.90780 ( 2331) link_ALPHA1-3 : bond 0.01060 ( 5) link_ALPHA1-3 : angle 1.88144 ( 15) link_ALPHA1-6 : bond 0.01055 ( 5) link_ALPHA1-6 : angle 1.83541 ( 15) link_BETA1-4 : bond 0.00405 ( 15) link_BETA1-4 : angle 1.35840 ( 45) link_NAG-ASN : bond 0.00199 ( 15) link_NAG-ASN : angle 1.28854 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3565.09 seconds wall clock time: 61 minutes 54.36 seconds (3714.36 seconds total)