Starting phenix.real_space_refine on Wed May 6 01:46:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v82_43015/05_2026/8v82_43015_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v82_43015/05_2026/8v82_43015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v82_43015/05_2026/8v82_43015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v82_43015/05_2026/8v82_43015.map" model { file = "/net/cci-nas-00/data/ceres_data/8v82_43015/05_2026/8v82_43015_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v82_43015/05_2026/8v82_43015_trim.cif" } resolution = 2.61 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= 0.010 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: 8 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 115 5.16 5 Cl 10 4.86 5 C 11450 2.51 5 N 2645 2.21 5 O 3200 1.98 5 H 15825 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33265 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6414 Chain: "B" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6414 Chain: "C" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6414 Chain: "D" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6414 Chain: "E" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6414 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 276 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 224 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 224 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 224 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 172 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 10.39, per 1000 atoms: 0.31 Number of scatterers: 33265 At special positions: 0 Unit cell: (102.505, 101.426, 161.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 5 19.99 Cl 10 17.00 S 115 16.00 P 15 15.00 O 3200 8.00 N 2645 7.00 C 11450 6.00 H 15825 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.05 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.05 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.05 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.05 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.05 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 602 " - " ASN A 67 " " NAG B 604 " - " ASN B 67 " " NAG C 604 " - " ASN C 67 " " NAG D 604 " - " ASN D 67 " " NAG E 604 " - " ASN E 67 " " NAG F 1 " - " ASN A 23 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN B 23 " " NAG I 1 " - " ASN B 110 " " NAG J 1 " - " ASN C 23 " " NAG K 1 " - " ASN C 110 " " NAG L 1 " - " ASN D 23 " " NAG M 1 " - " ASN D 110 " " NAG N 1 " - " ASN E 23 " " NAG O 1 " - " ASN E 110 " Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.3 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 44.5% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.724A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 214 through 227 removed outlier: 3.637A pdb=" N LEU A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 237 through 260 removed outlier: 4.569A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 409 through 465 Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.540A pdb=" N PHE A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.723A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.637A pdb=" N LEU B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 237 through 260 removed outlier: 4.568A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 409 through 465 Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.540A pdb=" N PHE B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.724A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.637A pdb=" N LEU C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 237 through 260 removed outlier: 4.569A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 409 through 465 Processing helix chain 'C' and resid 469 through 478 removed outlier: 3.540A pdb=" N PHE C 478 " --> pdb=" O VAL C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.723A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 227 removed outlier: 3.637A pdb=" N LEU D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 237 through 260 removed outlier: 4.569A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 409 through 465 Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.540A pdb=" N PHE D 478 " --> pdb=" O VAL D 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.724A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 227 removed outlier: 3.637A pdb=" N LEU E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 232 through 236 Processing helix chain 'E' and resid 237 through 260 removed outlier: 4.569A pdb=" N VAL E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 409 through 465 Processing helix chain 'E' and resid 469 through 478 removed outlier: 3.540A pdb=" N PHE E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 48 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP C 41 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR C 60 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR C 29 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.543A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.543A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.506A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP D 41 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR D 60 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR D 29 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.507A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.507A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL E 48 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP E 41 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR E 60 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR E 29 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.544A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) 971 hydrogen bonds defined for protein. 2838 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: 9.38 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 15785 1.05 - 1.25: 2620 1.25 - 1.46: 6618 1.46 - 1.67: 8487 1.67 - 1.87: 180 Bond restraints: 33690 Sorted by residual: bond pdb=" NZ LYS B 75 " pdb=" HZ3 LYS B 75 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" NZ LYS C 181 " pdb=" HZ2 LYS C 181 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS D 124 " pdb=" HZ2 LYS D 124 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS B 303 " pdb=" HZ3 LYS B 303 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS B 191 " pdb=" HZ1 LYS B 191 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 33685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 55600 2.55 - 5.10: 4485 5.10 - 7.64: 140 7.64 - 10.19: 0 10.19 - 12.74: 5 Bond angle restraints: 60230 Sorted by residual: angle pdb=" O11 POV D 605 " pdb=" P POV D 605 " pdb=" O12 POV D 605 " ideal model delta sigma weight residual 97.67 110.41 -12.74 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 POV A 603 " pdb=" P POV A 603 " pdb=" O12 POV A 603 " ideal model delta sigma weight residual 97.67 110.40 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 POV A 608 " pdb=" P POV A 608 " pdb=" O12 POV A 608 " ideal model delta sigma weight residual 97.67 110.39 -12.72 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 POV C 605 " pdb=" P POV C 605 " pdb=" O12 POV C 605 " ideal model delta sigma weight residual 97.67 110.38 -12.71 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 POV B 605 " pdb=" P POV B 605 " pdb=" O12 POV B 605 " ideal model delta sigma weight residual 97.67 110.38 -12.71 3.00e+00 1.11e-01 1.79e+01 ... (remaining 60225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.78: 16267 29.78 - 59.56: 568 59.56 - 89.35: 125 89.35 - 119.13: 35 119.13 - 148.91: 20 Dihedral angle restraints: 17015 sinusoidal: 9840 harmonic: 7175 Sorted by residual: dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N CYS A 190 " pdb=" CA CYS A 190 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N CYS B 190 " pdb=" CA CYS B 190 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 17012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2132 0.063 - 0.125: 481 0.125 - 0.188: 98 0.188 - 0.250: 14 0.250 - 0.313: 15 Chirality restraints: 2740 Sorted by residual: chirality pdb=" C1 EPJ E 607 " pdb=" C2 EPJ E 607 " pdb=" C6 EPJ E 607 " pdb=" C7 EPJ E 607 " both_signs ideal model delta sigma weight residual False -2.85 -2.54 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C1 EPJ B 608 " pdb=" C2 EPJ B 608 " pdb=" C6 EPJ B 608 " pdb=" C7 EPJ B 608 " both_signs ideal model delta sigma weight residual False -2.85 -2.54 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C1 EPJ A 606 " pdb=" C2 EPJ A 606 " pdb=" C6 EPJ A 606 " pdb=" C7 EPJ A 606 " both_signs ideal model delta sigma weight residual False -2.85 -2.54 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 2737 not shown) Planarity restraints: 4740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 604 " -0.285 2.00e-02 2.50e+03 2.45e-01 7.52e+02 pdb=" C7 NAG E 604 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG E 604 " 0.002 2.00e-02 2.50e+03 pdb=" N2 NAG E 604 " 0.418 2.00e-02 2.50e+03 pdb=" O7 NAG E 604 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " -0.284 2.00e-02 2.50e+03 2.45e-01 7.52e+02 pdb=" C7 NAG A 602 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.002 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " 0.418 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 604 " 0.284 2.00e-02 2.50e+03 2.45e-01 7.52e+02 pdb=" C7 NAG D 604 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG D 604 " -0.002 2.00e-02 2.50e+03 pdb=" N2 NAG D 604 " -0.418 2.00e-02 2.50e+03 pdb=" O7 NAG D 604 " 0.202 2.00e-02 2.50e+03 ... (remaining 4737 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 2776 2.25 - 2.84: 72383 2.84 - 3.43: 85644 3.43 - 4.01: 125031 4.01 - 4.60: 188563 Nonbonded interactions: 474397 Sorted by model distance: nonbonded pdb=" OE2 GLU B 18 " pdb=" HH TYR B 63 " model vdw 1.667 2.450 nonbonded pdb=" OE2 GLU E 18 " pdb=" HH TYR E 63 " model vdw 1.667 2.450 nonbonded pdb=" OE2 GLU C 18 " pdb=" HH TYR C 63 " model vdw 1.668 2.450 nonbonded pdb=" OE2 GLU A 18 " pdb=" HH TYR A 63 " model vdw 1.668 2.450 nonbonded pdb=" OE2 GLU D 18 " pdb=" HH TYR D 63 " model vdw 1.669 2.450 ... (remaining 474392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 478)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.150 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 38.890 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.008 0.066 17905 Z= 0.363 Angle : 1.050 12.742 24375 Z= 0.510 Chirality : 0.060 0.313 2740 Planarity : 0.012 0.245 2870 Dihedral : 19.392 148.910 7650 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.17), residues: 1955 helix: -0.50 (0.16), residues: 790 sheet: -1.05 (0.21), residues: 460 loop : -1.23 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 309 TYR 0.017 0.003 TYR B 273 PHE 0.012 0.002 PHE E 99 TRP 0.019 0.002 TRP D 307 HIS 0.004 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00794 (17865) covalent geometry : angle 1.03056 (24265) SS BOND : bond 0.01412 ( 10) SS BOND : angle 3.45459 ( 20) hydrogen bonds : bond 0.15759 ( 866) hydrogen bonds : angle 7.50685 ( 2838) link_BETA1-4 : bond 0.00362 ( 15) link_BETA1-4 : angle 2.09219 ( 45) link_NAG-ASN : bond 0.00483 ( 15) link_NAG-ASN : angle 3.85651 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 156 ASP cc_start: 0.7857 (t0) cc_final: 0.7592 (t0) REVERT: C 278 MET cc_start: 0.7930 (mtp) cc_final: 0.7680 (mtp) REVERT: D 57 MET cc_start: 0.8385 (mtm) cc_final: 0.7946 (mtm) REVERT: E 156 ASP cc_start: 0.7778 (t0) cc_final: 0.7458 (t0) REVERT: E 253 MET cc_start: 0.7881 (mmt) cc_final: 0.7653 (mtp) REVERT: E 278 MET cc_start: 0.7888 (mtp) cc_final: 0.7593 (mtp) REVERT: E 309 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6858 (ttt180) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 1.4768 time to fit residues: 375.0571 Evaluate side-chains 186 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125477 restraints weight = 67546.962| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.46 r_work: 0.3313 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17905 Z= 0.145 Angle : 0.628 6.078 24375 Z= 0.311 Chirality : 0.041 0.150 2740 Planarity : 0.005 0.034 2870 Dihedral : 19.226 140.334 3885 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.39 % Allowed : 6.67 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.17), residues: 1955 helix: 0.21 (0.16), residues: 805 sheet: -1.04 (0.21), residues: 465 loop : -0.95 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 309 TYR 0.016 0.001 TYR A 187 PHE 0.015 0.001 PHE C 274 TRP 0.013 0.001 TRP B 307 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00314 (17865) covalent geometry : angle 0.61230 (24265) SS BOND : bond 0.00890 ( 10) SS BOND : angle 1.74826 ( 20) hydrogen bonds : bond 0.04827 ( 866) hydrogen bonds : angle 5.54741 ( 2838) link_BETA1-4 : bond 0.00522 ( 15) link_BETA1-4 : angle 1.87779 ( 45) link_NAG-ASN : bond 0.00250 ( 15) link_NAG-ASN : angle 2.58892 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 189 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: B 40 MET cc_start: 0.8602 (mtp) cc_final: 0.8318 (mtp) REVERT: D 40 MET cc_start: 0.8454 (mtp) cc_final: 0.8222 (mtp) REVERT: D 57 MET cc_start: 0.8574 (mtm) cc_final: 0.8107 (mtm) REVERT: D 429 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7490 (mt-10) REVERT: E 278 MET cc_start: 0.8246 (mtp) cc_final: 0.7967 (mtp) REVERT: E 303 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7389 (tptp) outliers start: 7 outliers final: 1 residues processed: 191 average time/residue: 1.5352 time to fit residues: 322.4743 Evaluate side-chains 176 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 169 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.148723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124407 restraints weight = 59990.294| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.41 r_work: 0.3297 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17905 Z= 0.186 Angle : 0.612 6.016 24375 Z= 0.306 Chirality : 0.041 0.147 2740 Planarity : 0.005 0.035 2870 Dihedral : 16.635 125.222 3885 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.17 % Allowed : 7.96 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 1955 helix: 0.59 (0.17), residues: 805 sheet: -0.74 (0.21), residues: 465 loop : -0.79 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.016 0.002 TYR B 187 PHE 0.015 0.002 PHE C 99 TRP 0.011 0.002 TRP C 307 HIS 0.004 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00412 (17865) covalent geometry : angle 0.59510 (24265) SS BOND : bond 0.00864 ( 10) SS BOND : angle 1.64938 ( 20) hydrogen bonds : bond 0.04716 ( 866) hydrogen bonds : angle 5.31154 ( 2838) link_BETA1-4 : bond 0.00425 ( 15) link_BETA1-4 : angle 1.87235 ( 45) link_NAG-ASN : bond 0.00188 ( 15) link_NAG-ASN : angle 2.67605 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: B 174 ASP cc_start: 0.7856 (m-30) cc_final: 0.7544 (m-30) REVERT: C 253 MET cc_start: 0.8393 (mmt) cc_final: 0.8068 (mmt) REVERT: C 450 MET cc_start: 0.7991 (ttt) cc_final: 0.7690 (ttp) REVERT: C 466 SER cc_start: 0.8771 (p) cc_final: 0.8502 (p) REVERT: D 429 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7311 (mt-10) REVERT: E 278 MET cc_start: 0.8302 (mtp) cc_final: 0.8024 (mtp) outliers start: 3 outliers final: 2 residues processed: 189 average time/residue: 1.4781 time to fit residues: 306.4314 Evaluate side-chains 178 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 157 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124871 restraints weight = 60130.246| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.39 r_work: 0.3308 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17905 Z= 0.188 Angle : 0.587 5.654 24375 Z= 0.299 Chirality : 0.040 0.146 2740 Planarity : 0.005 0.036 2870 Dihedral : 15.763 113.414 3885 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.39 % Allowed : 8.29 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.18), residues: 1955 helix: 0.71 (0.17), residues: 810 sheet: -0.61 (0.22), residues: 465 loop : -0.75 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.012 0.002 TYR B 187 PHE 0.014 0.002 PHE B 99 TRP 0.011 0.002 TRP E 307 HIS 0.004 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00414 (17865) covalent geometry : angle 0.57088 (24265) SS BOND : bond 0.00862 ( 10) SS BOND : angle 1.59332 ( 20) hydrogen bonds : bond 0.04470 ( 866) hydrogen bonds : angle 5.19423 ( 2838) link_BETA1-4 : bond 0.00367 ( 15) link_BETA1-4 : angle 1.65265 ( 45) link_NAG-ASN : bond 0.00111 ( 15) link_NAG-ASN : angle 2.66579 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: B 174 ASP cc_start: 0.7874 (m-30) cc_final: 0.7565 (m-30) REVERT: C 253 MET cc_start: 0.8306 (mmt) cc_final: 0.8089 (mmt) REVERT: C 278 MET cc_start: 0.8234 (mtt) cc_final: 0.7985 (mtp) REVERT: C 450 MET cc_start: 0.8005 (ttt) cc_final: 0.7703 (ttp) REVERT: D 429 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7350 (mt-10) REVERT: E 278 MET cc_start: 0.8324 (mtp) cc_final: 0.8069 (mtp) REVERT: E 445 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.6507 (m-30) outliers start: 7 outliers final: 4 residues processed: 181 average time/residue: 1.5749 time to fit residues: 312.9842 Evaluate side-chains 180 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 102 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 62 optimal weight: 0.0270 chunk 110 optimal weight: 6.9990 chunk 143 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.125849 restraints weight = 62245.391| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.42 r_work: 0.3322 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17905 Z= 0.147 Angle : 0.549 5.509 24375 Z= 0.277 Chirality : 0.039 0.145 2740 Planarity : 0.004 0.037 2870 Dihedral : 15.150 101.595 3885 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.39 % Allowed : 8.46 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.18), residues: 1955 helix: 1.06 (0.17), residues: 795 sheet: -0.58 (0.22), residues: 465 loop : -0.67 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 446 TYR 0.009 0.002 TYR D 128 PHE 0.014 0.001 PHE C 274 TRP 0.010 0.001 TRP E 307 HIS 0.003 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00319 (17865) covalent geometry : angle 0.53429 (24265) SS BOND : bond 0.00842 ( 10) SS BOND : angle 1.41980 ( 20) hydrogen bonds : bond 0.04167 ( 866) hydrogen bonds : angle 4.99432 ( 2838) link_BETA1-4 : bond 0.00322 ( 15) link_BETA1-4 : angle 1.39186 ( 45) link_NAG-ASN : bond 0.00065 ( 15) link_NAG-ASN : angle 2.54305 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: B 174 ASP cc_start: 0.7725 (m-30) cc_final: 0.7411 (m-30) REVERT: B 445 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.6337 (m-30) REVERT: C 278 MET cc_start: 0.8274 (mtt) cc_final: 0.8013 (mtp) REVERT: C 450 MET cc_start: 0.8005 (ttt) cc_final: 0.7711 (ttp) REVERT: D 429 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7321 (mt-10) REVERT: E 185 ARG cc_start: 0.6591 (ttt180) cc_final: 0.6373 (ttt180) REVERT: E 278 MET cc_start: 0.8277 (mtp) cc_final: 0.8032 (mtp) outliers start: 7 outliers final: 3 residues processed: 179 average time/residue: 1.5668 time to fit residues: 306.4645 Evaluate side-chains 174 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 15 optimal weight: 3.9990 chunk 168 optimal weight: 0.0270 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123686 restraints weight = 66442.611| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.47 r_work: 0.3288 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17905 Z= 0.212 Angle : 0.598 5.901 24375 Z= 0.305 Chirality : 0.041 0.149 2740 Planarity : 0.005 0.043 2870 Dihedral : 15.090 99.388 3885 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.28 % Allowed : 8.74 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.18), residues: 1955 helix: 1.03 (0.17), residues: 795 sheet: -0.46 (0.22), residues: 460 loop : -0.73 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.013 0.002 TYR D 128 PHE 0.016 0.002 PHE E 99 TRP 0.012 0.002 TRP E 307 HIS 0.004 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00473 (17865) covalent geometry : angle 0.58332 (24265) SS BOND : bond 0.00855 ( 10) SS BOND : angle 1.64449 ( 20) hydrogen bonds : bond 0.04520 ( 866) hydrogen bonds : angle 5.15386 ( 2838) link_BETA1-4 : bond 0.00262 ( 15) link_BETA1-4 : angle 1.41691 ( 45) link_NAG-ASN : bond 0.00159 ( 15) link_NAG-ASN : angle 2.65242 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 174 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: B 174 ASP cc_start: 0.7940 (m-30) cc_final: 0.7685 (m-30) REVERT: B 445 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6423 (m-30) REVERT: C 278 MET cc_start: 0.8374 (mtt) cc_final: 0.8139 (mtp) REVERT: C 450 MET cc_start: 0.8019 (ttt) cc_final: 0.7719 (ttp) REVERT: D 234 ASP cc_start: 0.7731 (m-30) cc_final: 0.7477 (m-30) REVERT: D 429 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7375 (mt-10) REVERT: E 278 MET cc_start: 0.8314 (mtp) cc_final: 0.8111 (mtp) outliers start: 5 outliers final: 3 residues processed: 174 average time/residue: 1.5958 time to fit residues: 304.7541 Evaluate side-chains 176 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 10 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 69 optimal weight: 0.0010 chunk 61 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126877 restraints weight = 61639.033| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.42 r_work: 0.3336 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17905 Z= 0.124 Angle : 0.531 6.022 24375 Z= 0.268 Chirality : 0.039 0.145 2740 Planarity : 0.004 0.039 2870 Dihedral : 14.420 88.805 3885 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.28 % Allowed : 8.85 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 1955 helix: 1.19 (0.17), residues: 795 sheet: -0.44 (0.22), residues: 460 loop : -0.57 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.009 0.001 TYR E 117 PHE 0.010 0.001 PHE A 319 TRP 0.009 0.001 TRP D 307 HIS 0.002 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00266 (17865) covalent geometry : angle 0.51767 (24265) SS BOND : bond 0.00823 ( 10) SS BOND : angle 1.41246 ( 20) hydrogen bonds : bond 0.04002 ( 866) hydrogen bonds : angle 4.86534 ( 2838) link_BETA1-4 : bond 0.00327 ( 15) link_BETA1-4 : angle 1.30346 ( 45) link_NAG-ASN : bond 0.00078 ( 15) link_NAG-ASN : angle 2.40580 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 ASP cc_start: 0.7694 (m-30) cc_final: 0.7454 (m-30) REVERT: D 234 ASP cc_start: 0.7685 (m-30) cc_final: 0.7430 (m-30) REVERT: E 278 MET cc_start: 0.8292 (mtp) cc_final: 0.8064 (mtp) outliers start: 5 outliers final: 3 residues processed: 182 average time/residue: 1.5295 time to fit residues: 304.7699 Evaluate side-chains 183 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 180 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 105 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 182 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.125326 restraints weight = 62151.139| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.42 r_work: 0.3301 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17905 Z= 0.170 Angle : 0.563 5.902 24375 Z= 0.285 Chirality : 0.039 0.144 2740 Planarity : 0.005 0.037 2870 Dihedral : 14.266 83.988 3885 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.28 % Allowed : 8.96 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 1955 helix: 1.21 (0.17), residues: 795 sheet: -0.37 (0.23), residues: 460 loop : -0.58 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 446 TYR 0.011 0.002 TYR E 187 PHE 0.018 0.001 PHE C 274 TRP 0.011 0.001 TRP D 307 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00376 (17865) covalent geometry : angle 0.54893 (24265) SS BOND : bond 0.00826 ( 10) SS BOND : angle 1.55936 ( 20) hydrogen bonds : bond 0.04213 ( 866) hydrogen bonds : angle 4.95368 ( 2838) link_BETA1-4 : bond 0.00268 ( 15) link_BETA1-4 : angle 1.32466 ( 45) link_NAG-ASN : bond 0.00097 ( 15) link_NAG-ASN : angle 2.46627 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 183 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8384 (ttmm) cc_final: 0.8171 (mtpt) REVERT: B 174 ASP cc_start: 0.7896 (m-30) cc_final: 0.7647 (m-30) REVERT: B 445 ASP cc_start: 0.6501 (OUTLIER) cc_final: 0.6227 (m-30) REVERT: D 234 ASP cc_start: 0.7678 (m-30) cc_final: 0.7420 (m-30) REVERT: E 278 MET cc_start: 0.8307 (mtp) cc_final: 0.8084 (mtp) outliers start: 5 outliers final: 4 residues processed: 184 average time/residue: 1.4792 time to fit residues: 298.5771 Evaluate side-chains 181 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 93 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123665 restraints weight = 64735.050| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.45 r_work: 0.3289 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17905 Z= 0.219 Angle : 0.602 6.299 24375 Z= 0.308 Chirality : 0.041 0.149 2740 Planarity : 0.005 0.048 2870 Dihedral : 14.248 85.720 3885 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.45 % Allowed : 8.91 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 1955 helix: 1.10 (0.17), residues: 795 sheet: -0.38 (0.22), residues: 460 loop : -0.65 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 446 TYR 0.013 0.002 TYR E 187 PHE 0.025 0.002 PHE C 274 TRP 0.013 0.002 TRP D 307 HIS 0.004 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00490 (17865) covalent geometry : angle 0.58790 (24265) SS BOND : bond 0.00817 ( 10) SS BOND : angle 1.67949 ( 20) hydrogen bonds : bond 0.04521 ( 866) hydrogen bonds : angle 5.13576 ( 2838) link_BETA1-4 : bond 0.00236 ( 15) link_BETA1-4 : angle 1.39914 ( 45) link_NAG-ASN : bond 0.00162 ( 15) link_NAG-ASN : angle 2.63375 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.860 Fit side-chains REVERT: B 445 ASP cc_start: 0.6556 (OUTLIER) cc_final: 0.6263 (m-30) REVERT: D 234 ASP cc_start: 0.7687 (m-30) cc_final: 0.7421 (m-30) REVERT: D 429 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7306 (mt-10) REVERT: E 278 MET cc_start: 0.8325 (mtp) cc_final: 0.8088 (mtp) REVERT: E 445 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6443 (m-30) outliers start: 8 outliers final: 4 residues processed: 173 average time/residue: 1.5365 time to fit residues: 293.2221 Evaluate side-chains 176 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 170 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 115 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.150222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126424 restraints weight = 62524.128| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.43 r_work: 0.3328 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17905 Z= 0.130 Angle : 0.540 7.339 24375 Z= 0.272 Chirality : 0.039 0.150 2740 Planarity : 0.004 0.038 2870 Dihedral : 13.505 80.447 3885 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.28 % Allowed : 9.13 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 1955 helix: 1.24 (0.17), residues: 795 sheet: -0.47 (0.22), residues: 465 loop : -0.51 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 446 TYR 0.010 0.001 TYR A 273 PHE 0.019 0.001 PHE C 274 TRP 0.011 0.001 TRP D 307 HIS 0.002 0.001 HIS D 295 Details of bonding type rmsd covalent geometry : bond 0.00281 (17865) covalent geometry : angle 0.52695 (24265) SS BOND : bond 0.00830 ( 10) SS BOND : angle 1.42571 ( 20) hydrogen bonds : bond 0.03998 ( 866) hydrogen bonds : angle 4.86014 ( 2838) link_BETA1-4 : bond 0.00300 ( 15) link_BETA1-4 : angle 1.28028 ( 45) link_NAG-ASN : bond 0.00085 ( 15) link_NAG-ASN : angle 2.35841 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 179 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8182 (mtpt) REVERT: B 174 ASP cc_start: 0.7687 (m-30) cc_final: 0.7475 (m-30) REVERT: B 445 ASP cc_start: 0.6492 (OUTLIER) cc_final: 0.6231 (m-30) REVERT: D 234 ASP cc_start: 0.7680 (m-30) cc_final: 0.7410 (m-30) REVERT: D 429 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7326 (mt-10) REVERT: E 278 MET cc_start: 0.8297 (mtp) cc_final: 0.8053 (mtp) REVERT: E 445 ASP cc_start: 0.6613 (OUTLIER) cc_final: 0.6399 (m-30) outliers start: 5 outliers final: 4 residues processed: 180 average time/residue: 1.4786 time to fit residues: 292.3348 Evaluate side-chains 184 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 2 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.149290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125057 restraints weight = 67518.825| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.47 r_work: 0.3292 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17905 Z= 0.160 Angle : 0.554 7.037 24375 Z= 0.281 Chirality : 0.039 0.145 2740 Planarity : 0.005 0.037 2870 Dihedral : 13.313 81.362 3885 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.28 % Allowed : 9.41 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 1955 helix: 1.28 (0.17), residues: 795 sheet: -0.42 (0.22), residues: 465 loop : -0.53 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.011 0.002 TYR A 273 PHE 0.026 0.001 PHE C 274 TRP 0.011 0.001 TRP D 307 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00354 (17865) covalent geometry : angle 0.54081 (24265) SS BOND : bond 0.00825 ( 10) SS BOND : angle 1.53879 ( 20) hydrogen bonds : bond 0.04147 ( 866) hydrogen bonds : angle 4.91409 ( 2838) link_BETA1-4 : bond 0.00278 ( 15) link_BETA1-4 : angle 1.29678 ( 45) link_NAG-ASN : bond 0.00087 ( 15) link_NAG-ASN : angle 2.39621 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11099.03 seconds wall clock time: 188 minutes 6.37 seconds (11286.37 seconds total)