Starting phenix.real_space_refine on Mon Jul 6 10:50:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v8a_43032/07_2026/8v8a_43032_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v8a_43032/07_2026/8v8a_43032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v8a_43032/07_2026/8v8a_43032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v8a_43032/07_2026/8v8a_43032.map" model { file = "/net/cci-nas-00/data/ceres_data/8v8a_43032/07_2026/8v8a_43032_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v8a_43032/07_2026/8v8a_43032_trim.cif" } resolution = 2.19 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= 0.125 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 120 5.16 5 Cl 10 4.86 5 C 11510 2.51 5 N 2650 2.21 5 O 3315 1.98 5 H 15935 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33560 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6391 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: 6370 Chain: "B" Number of atoms: 6391 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: 6370 Chain: "C" Number of atoms: 6391 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: 6370 Chain: "D" Number of atoms: 6391 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: 6370 Chain: "E" Number of atoms: 6391 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: 6370 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: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 222 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 222 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 222 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 222 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 222 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Time building chain proxies: 9.26, per 1000 atoms: 0.28 Number of scatterers: 33560 At special positions: 0 Unit cell: (99, 101.475, 163.35, 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 120 16.00 P 15 15.00 O 3315 8.00 N 2650 7.00 C 11510 6.00 H 15935 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=2.04 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=2.04 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=2.04 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=2.04 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=2.04 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: 2.94 Conformation dependent library (CDL) restraints added in 1.5 seconds 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 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: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 214 through 227 removed outlier: 3.809A pdb=" N ALA A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.686A 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 258 removed outlier: 3.779A pdb=" N THR A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.856A 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 466 Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.809A pdb=" N ALA B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.685A 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 258 removed outlier: 3.779A pdb=" N THR B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.856A 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 466 Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.809A pdb=" N ALA C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.686A 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 258 removed outlier: 3.779A pdb=" N THR C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.856A 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 466 Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 227 removed outlier: 3.809A pdb=" N ALA D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 3.686A 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 258 removed outlier: 3.779A pdb=" N THR D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.856A 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 466 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 227 removed outlier: 3.809A pdb=" N ALA E 225 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) removed outlier: 3.686A 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 258 removed outlier: 3.779A pdb=" N THR E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.856A 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 466 Processing helix chain 'E' and resid 469 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.086A 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: 4.086A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.875A 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: 4.420A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.721A 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: 4.420A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 185 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.085A 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: 4.085A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.875A 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: 4.419A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.720A 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: 4.419A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 185 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.086A 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: 4.086A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 48 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP C 41 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR C 60 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.874A 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: 4.420A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.721A 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: 4.420A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG C 185 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.086A 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: 4.086A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP D 41 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR D 60 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.875A 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: 4.420A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.721A 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: 4.420A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG D 185 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.085A 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: 4.085A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL E 48 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP E 41 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR E 60 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 6.876A 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: 4.420A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.721A 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: 4.420A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG E 185 " --> pdb=" O TYR E 194 " (cutoff:3.500A) 966 hydrogen bonds defined for protein. 2818 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: 9.67 Time building geometry restraints manager: 4.10 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: 15910 1.05 - 1.25: 2620 1.25 - 1.46: 6716 1.46 - 1.67: 8469 1.67 - 1.87: 190 Bond restraints: 33905 Sorted by residual: bond pdb=" NZ LYS E 303 " pdb=" HZ1 LYS E 303 " 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 D 191 " pdb=" HZ3 LYS D 191 " 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=" HZ3 LYS D 124 " 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 E 181 " pdb=" HZ1 LYS E 181 " 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 D 181 " pdb=" HZ1 LYS D 181 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 33900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 55023 2.35 - 4.69: 5343 4.69 - 7.04: 279 7.04 - 9.38: 20 9.38 - 11.73: 15 Bond angle restraints: 60680 Sorted by residual: angle pdb=" C2 POV C 601 " pdb=" O21 POV C 601 " pdb=" C21 POV C 601 " ideal model delta sigma weight residual 119.46 131.19 -11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C2 POV B 601 " pdb=" O21 POV B 601 " pdb=" C21 POV B 601 " ideal model delta sigma weight residual 119.46 131.18 -11.72 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C2 POV D 601 " pdb=" O21 POV D 601 " pdb=" C21 POV D 601 " ideal model delta sigma weight residual 119.46 131.17 -11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C2 POV A 607 " pdb=" O21 POV A 607 " pdb=" C21 POV A 607 " ideal model delta sigma weight residual 119.46 131.16 -11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C2 POV E 601 " pdb=" O21 POV E 601 " pdb=" C21 POV E 601 " ideal model delta sigma weight residual 119.46 131.16 -11.70 3.00e+00 1.11e-01 1.52e+01 ... (remaining 60675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.55: 16221 29.55 - 59.11: 754 59.11 - 88.66: 110 88.66 - 118.22: 45 118.22 - 147.77: 15 Dihedral angle restraints: 17145 sinusoidal: 9910 harmonic: 7235 Sorted by residual: 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 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual -180.00 -153.88 -26.12 0 5.00e+00 4.00e-02 2.73e+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 -153.89 -26.11 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 17142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2280 0.073 - 0.146: 390 0.146 - 0.220: 71 0.220 - 0.293: 14 0.293 - 0.366: 5 Chirality restraints: 2760 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.76e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.59e+01 chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.54e+01 ... (remaining 2757 not shown) Planarity restraints: 4775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 427 " 0.073 2.00e-02 2.50e+03 6.31e-02 5.98e+01 pdb=" CD GLN D 427 " -0.081 2.00e-02 2.50e+03 pdb=" OE1 GLN D 427 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN D 427 " -0.008 2.00e-02 2.50e+03 pdb="HE21 GLN D 427 " -0.060 2.00e-02 2.50e+03 pdb="HE22 GLN D 427 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 427 " 0.073 2.00e-02 2.50e+03 6.31e-02 5.98e+01 pdb=" CD GLN C 427 " -0.081 2.00e-02 2.50e+03 pdb=" OE1 GLN C 427 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN C 427 " -0.009 2.00e-02 2.50e+03 pdb="HE21 GLN C 427 " -0.060 2.00e-02 2.50e+03 pdb="HE22 GLN C 427 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 427 " 0.073 2.00e-02 2.50e+03 6.31e-02 5.97e+01 pdb=" CD GLN E 427 " -0.081 2.00e-02 2.50e+03 pdb=" OE1 GLN E 427 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN E 427 " -0.009 2.00e-02 2.50e+03 pdb="HE21 GLN E 427 " -0.060 2.00e-02 2.50e+03 pdb="HE22 GLN E 427 " 0.090 2.00e-02 2.50e+03 ... (remaining 4772 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 947 2.15 - 2.76: 60884 2.76 - 3.38: 97097 3.38 - 3.99: 132237 3.99 - 4.60: 199966 Nonbonded interactions: 491131 Sorted by model distance: nonbonded pdb=" HZ1 LYS E 144 " pdb=" HH TYR E 187 " model vdw 1.541 2.100 nonbonded pdb=" HZ1 LYS B 144 " pdb=" HH TYR B 187 " model vdw 1.541 2.100 nonbonded pdb=" HZ1 LYS A 144 " pdb=" HH TYR A 187 " model vdw 1.541 2.100 nonbonded pdb=" HZ1 LYS D 144 " pdb=" HH TYR D 187 " model vdw 1.541 2.100 nonbonded pdb=" HZ1 LYS C 144 " pdb=" HH TYR C 187 " model vdw 1.541 2.100 ... (remaining 491126 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 55 or resid 57 through 83 or resid 85 through 11 \ 3 or resid 115 through 252 or resid 254 through 478)) selection = (chain 'B' and (resid 1 through 55 or resid 57 through 83 or resid 85 through 11 \ 3 or resid 115 through 252 or resid 254 through 478)) selection = (chain 'C' and (resid 1 through 55 or resid 57 through 83 or resid 85 through 11 \ 3 or resid 115 through 252 or resid 254 through 478)) selection = (chain 'D' and (resid 1 through 55 or resid 57 through 83 or resid 85 through 11 \ 3 or resid 115 through 252 or resid 254 through 478)) selection = (chain 'E' and (resid 1 through 55 or resid 57 through 83 or resid 85 through 11 \ 3 or resid 115 through 252 or resid 254 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=0.99 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: 3.710 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: 0.200 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 38.620 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 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:8.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 17995 Z= 0.340 Angle : 1.111 11.726 24520 Z= 0.550 Chirality : 0.060 0.366 2760 Planarity : 0.007 0.052 2890 Dihedral : 19.917 147.774 7715 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.56 % Allowed : 0.28 % Favored : 99.17 % 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: -0.64 (0.17), residues: 1970 helix: -0.25 (0.16), residues: 790 sheet: -0.77 (0.21), residues: 490 loop : -0.00 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 98 TYR 0.018 0.004 TYR D 273 PHE 0.022 0.003 PHE E 99 TRP 0.015 0.003 TRP D 153 HIS 0.009 0.004 HIS E 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.34 (17955) covalent geometry : angle 1.09304 / 0.55 (24410) SS BOND : bond 0.01340 / 0.73 ( 10) SS BOND : angle 3.08294 / 1.89 ( 20) hydrogen bonds : bond 0.17811 / 11.34 ( 861) hydrogen bonds : angle 7.32058 / 5.13 ( 2818) link_BETA1-4 : bond 0.00718 / 0.37 ( 15) link_BETA1-4 : angle 2.48631 / 1.63 ( 45) link_NAG-ASN : bond 0.03722 / 1.84 ( 15) link_NAG-ASN : angle 3.77312 / 2.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 270 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.7905 (mmt) cc_final: 0.7668 (mmt) REVERT: A 428 ASP cc_start: 0.7866 (m-30) cc_final: 0.7643 (m-30) REVERT: C 40 MET cc_start: 0.8089 (mtp) cc_final: 0.7848 (mtm) REVERT: C 454 VAL cc_start: 0.7964 (t) cc_final: 0.7751 (p) REVERT: E 57 MET cc_start: 0.8505 (mtm) cc_final: 0.8239 (mtp) outliers start: 5 outliers final: 5 residues processed: 275 average time/residue: 1.2867 time to fit residues: 396.2465 Evaluate side-chains 246 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 241 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 GLN A 272 GLN B 52 ASN B 272 GLN C 272 GLN D 52 ASN D 272 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.170271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.148590 restraints weight = 61716.331| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 0.82 r_work: 0.3331 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17995 Z= 0.145 Angle : 0.650 6.904 24520 Z= 0.328 Chirality : 0.043 0.170 2760 Planarity : 0.005 0.044 2890 Dihedral : 18.686 139.862 3930 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.17 % Allowed : 4.00 % Favored : 94.83 % 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: 0.58 (0.18), residues: 1970 helix: 1.24 (0.17), residues: 795 sheet: -0.44 (0.23), residues: 480 loop : 0.22 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 446 TYR 0.010 0.002 TYR C 273 PHE 0.014 0.001 PHE B 455 TRP 0.008 0.001 TRP A 315 HIS 0.004 0.001 HIS A 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (17955) covalent geometry : angle 0.63495 / 0.32 (24410) SS BOND : bond 0.00880 / 0.47 ( 10) SS BOND : angle 1.64899 / 0.96 ( 20) hydrogen bonds : bond 0.05133 / 3.34 ( 861) hydrogen bonds : angle 5.31865 / 3.72 ( 2818) link_BETA1-4 : bond 0.00248 / 0.15 ( 15) link_BETA1-4 : angle 1.98817 / 1.44 ( 45) link_NAG-ASN : bond 0.00179 / 0.10 ( 15) link_NAG-ASN : angle 2.49717 / 1.64 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8294 (ttpt) cc_final: 0.8027 (tppp) REVERT: A 98 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7352 (ptt90) REVERT: B 98 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7275 (ptt90) REVERT: B 156 ASP cc_start: 0.8542 (t0) cc_final: 0.8234 (t0) REVERT: C 40 MET cc_start: 0.8421 (mtp) cc_final: 0.8175 (mtm) REVERT: C 98 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7310 (ptt90) REVERT: C 156 ASP cc_start: 0.8253 (t70) cc_final: 0.7936 (t70) REVERT: D 98 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7244 (ptt90) REVERT: D 450 MET cc_start: 0.8222 (mmp) cc_final: 0.7926 (ttt) REVERT: D 461 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.8015 (mp) REVERT: E 12 LYS cc_start: 0.8328 (ttpt) cc_final: 0.8105 (tppp) REVERT: E 98 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7277 (ptt90) REVERT: E 156 ASP cc_start: 0.8436 (t0) cc_final: 0.8130 (t0) REVERT: E 260 MET cc_start: 0.8183 (mmp) cc_final: 0.7919 (mmp) outliers start: 16 outliers final: 3 residues processed: 271 average time/residue: 1.2419 time to fit residues: 380.8037 Evaluate side-chains 248 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 239 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 119 optimal weight: 0.0570 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.168404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.146587 restraints weight = 53234.038| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 0.82 r_work: 0.3330 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17995 Z= 0.164 Angle : 0.629 4.539 24520 Z= 0.321 Chirality : 0.043 0.172 2760 Planarity : 0.005 0.046 2890 Dihedral : 16.849 133.288 3930 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.11 % Allowed : 5.44 % Favored : 93.44 % 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: 0.84 (0.18), residues: 1970 helix: 1.44 (0.17), residues: 805 sheet: -0.36 (0.23), residues: 475 loop : 0.39 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 446 TYR 0.013 0.002 TYR A 273 PHE 0.016 0.002 PHE C 99 TRP 0.009 0.001 TRP D 307 HIS 0.005 0.002 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (17955) covalent geometry : angle 0.61692 / 0.32 (24410) SS BOND : bond 0.00878 / 0.47 ( 10) SS BOND : angle 1.68901 / 0.97 ( 20) hydrogen bonds : bond 0.05377 / 3.48 ( 861) hydrogen bonds : angle 5.22146 / 3.65 ( 2818) link_BETA1-4 : bond 0.00330 / 0.18 ( 15) link_BETA1-4 : angle 1.70601 / 1.21 ( 45) link_NAG-ASN : bond 0.00290 / 0.18 ( 15) link_NAG-ASN : angle 2.25812 / 1.46 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7932 (pt0) cc_final: 0.7703 (pt0) REVERT: A 156 ASP cc_start: 0.8496 (t0) cc_final: 0.8182 (t0) REVERT: A 260 MET cc_start: 0.8203 (mmp) cc_final: 0.7930 (mmt) REVERT: B 156 ASP cc_start: 0.8604 (t0) cc_final: 0.8267 (t0) REVERT: C 40 MET cc_start: 0.8409 (mtp) cc_final: 0.8134 (mtm) REVERT: C 81 ASP cc_start: 0.8354 (t0) cc_final: 0.8126 (t0) REVERT: C 156 ASP cc_start: 0.8306 (t70) cc_final: 0.7972 (t70) REVERT: D 156 ASP cc_start: 0.8429 (t0) cc_final: 0.8086 (t0) REVERT: D 450 MET cc_start: 0.8270 (mmp) cc_final: 0.7880 (ttt) REVERT: E 12 LYS cc_start: 0.8346 (ttpt) cc_final: 0.8134 (tppp) REVERT: E 156 ASP cc_start: 0.8503 (t0) cc_final: 0.8179 (t0) REVERT: E 450 MET cc_start: 0.8257 (mmp) cc_final: 0.7895 (ttt) outliers start: 15 outliers final: 6 residues processed: 243 average time/residue: 1.3151 time to fit residues: 358.7251 Evaluate side-chains 240 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 234 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 162 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 0.0470 chunk 135 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 181 optimal weight: 0.0370 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.170074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.148283 restraints weight = 53709.353| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 0.81 r_work: 0.3343 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17995 Z= 0.128 Angle : 0.561 6.059 24520 Z= 0.287 Chirality : 0.040 0.154 2760 Planarity : 0.004 0.048 2890 Dihedral : 15.300 131.057 3930 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.83 % Allowed : 5.89 % Favored : 93.28 % 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: 1.03 (0.18), residues: 1970 helix: 1.62 (0.17), residues: 810 sheet: -0.29 (0.23), residues: 470 loop : 0.47 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 446 TYR 0.012 0.002 TYR A 273 PHE 0.013 0.001 PHE A 455 TRP 0.009 0.001 TRP D 307 HIS 0.003 0.001 HIS C 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (17955) covalent geometry : angle 0.54800 / 0.28 (24410) SS BOND : bond 0.00795 / 0.43 ( 10) SS BOND : angle 1.48915 / 0.86 ( 20) hydrogen bonds : bond 0.04534 / 2.96 ( 861) hydrogen bonds : angle 4.96473 / 3.47 ( 2818) link_BETA1-4 : bond 0.00332 / 0.18 ( 15) link_BETA1-4 : angle 1.47672 / 1.06 ( 45) link_NAG-ASN : bond 0.00209 / 0.14 ( 15) link_NAG-ASN : angle 2.27438 / 1.49 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 240 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7870 (tppp) REVERT: A 38 GLN cc_start: 0.7903 (pt0) cc_final: 0.7643 (pt0) REVERT: A 156 ASP cc_start: 0.8412 (t0) cc_final: 0.8142 (t0) REVERT: B 98 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7185 (ptt90) REVERT: B 156 ASP cc_start: 0.8493 (t0) cc_final: 0.8238 (t0) REVERT: C 40 MET cc_start: 0.8397 (mtp) cc_final: 0.8149 (mtm) REVERT: C 156 ASP cc_start: 0.8203 (t70) cc_final: 0.7845 (t70) REVERT: D 156 ASP cc_start: 0.8340 (t0) cc_final: 0.8067 (t0) REVERT: E 12 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7988 (tppp) REVERT: E 57 MET cc_start: 0.8686 (mtm) cc_final: 0.8397 (mtp) REVERT: E 260 MET cc_start: 0.8459 (mmp) cc_final: 0.8183 (mmp) outliers start: 10 outliers final: 6 residues processed: 243 average time/residue: 1.2766 time to fit residues: 350.4013 Evaluate side-chains 240 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 233 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 56 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 119 optimal weight: 0.0670 chunk 160 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.169901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.148721 restraints weight = 58822.779| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 0.79 r_work: 0.3340 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17995 Z= 0.130 Angle : 0.559 5.203 24520 Z= 0.286 Chirality : 0.040 0.165 2760 Planarity : 0.004 0.046 2890 Dihedral : 14.956 128.460 3930 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.89 % Allowed : 6.11 % Favored : 93.00 % 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: 1.13 (0.18), residues: 1970 helix: 1.69 (0.17), residues: 810 sheet: -0.31 (0.23), residues: 475 loop : 0.61 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 446 TYR 0.012 0.002 TYR A 273 PHE 0.011 0.001 PHE E 99 TRP 0.009 0.001 TRP D 307 HIS 0.003 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (17955) covalent geometry : angle 0.54797 / 0.28 (24410) SS BOND : bond 0.00772 / 0.42 ( 10) SS BOND : angle 1.43631 / 0.83 ( 20) hydrogen bonds : bond 0.04594 / 3.00 ( 861) hydrogen bonds : angle 4.93544 / 3.45 ( 2818) link_BETA1-4 : bond 0.00302 / 0.17 ( 15) link_BETA1-4 : angle 1.27891 / 0.92 ( 45) link_NAG-ASN : bond 0.00202 / 0.13 ( 15) link_NAG-ASN : angle 2.22667 / 1.46 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 234 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7918 (tppp) REVERT: A 38 GLN cc_start: 0.7967 (pt0) cc_final: 0.7685 (pt0) REVERT: A 156 ASP cc_start: 0.8484 (t0) cc_final: 0.8149 (t0) REVERT: B 98 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7213 (ptt90) REVERT: B 156 ASP cc_start: 0.8540 (t0) cc_final: 0.8232 (t0) REVERT: C 40 MET cc_start: 0.8396 (mtp) cc_final: 0.8155 (mtm) REVERT: C 156 ASP cc_start: 0.8283 (t70) cc_final: 0.7848 (t70) REVERT: D 156 ASP cc_start: 0.8427 (t0) cc_final: 0.8075 (t0) REVERT: E 12 LYS cc_start: 0.8247 (ttpt) cc_final: 0.8043 (tppp) REVERT: E 57 MET cc_start: 0.8696 (mtm) cc_final: 0.8433 (mtp) REVERT: E 156 ASP cc_start: 0.8461 (t0) cc_final: 0.8221 (t0) outliers start: 11 outliers final: 5 residues processed: 238 average time/residue: 1.3530 time to fit residues: 363.0220 Evaluate side-chains 235 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 229 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 108 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 133 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.167920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.146187 restraints weight = 57213.707| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 0.84 r_work: 0.3330 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17995 Z= 0.166 Angle : 0.604 5.100 24520 Z= 0.312 Chirality : 0.041 0.167 2760 Planarity : 0.005 0.050 2890 Dihedral : 14.935 126.387 3930 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.89 % Allowed : 6.44 % Favored : 92.67 % 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: 1.05 (0.18), residues: 1970 helix: 1.62 (0.17), residues: 810 sheet: -0.36 (0.23), residues: 475 loop : 0.59 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 446 TYR 0.015 0.002 TYR A 273 PHE 0.017 0.002 PHE C 99 TRP 0.009 0.001 TRP D 307 HIS 0.006 0.002 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (17955) covalent geometry : angle 0.59414 / 0.31 (24410) SS BOND : bond 0.00822 / 0.44 ( 10) SS BOND : angle 1.57911 / 0.91 ( 20) hydrogen bonds : bond 0.05071 / 3.30 ( 861) hydrogen bonds : angle 5.06993 / 3.55 ( 2818) link_BETA1-4 : bond 0.00265 / 0.16 ( 15) link_BETA1-4 : angle 1.30425 / 0.94 ( 45) link_NAG-ASN : bond 0.00299 / 0.19 ( 15) link_NAG-ASN : angle 2.17980 / 1.41 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 237 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.8464 (t0) cc_final: 0.8175 (t0) REVERT: B 98 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7217 (ptt90) REVERT: B 156 ASP cc_start: 0.8549 (t0) cc_final: 0.8246 (t0) REVERT: C 40 MET cc_start: 0.8418 (mtp) cc_final: 0.8184 (mtm) REVERT: D 156 ASP cc_start: 0.8408 (t0) cc_final: 0.8075 (t0) REVERT: E 12 LYS cc_start: 0.8253 (ttpt) cc_final: 0.8043 (tppp) REVERT: E 57 MET cc_start: 0.8700 (mtm) cc_final: 0.8376 (mtp) REVERT: E 156 ASP cc_start: 0.8442 (t0) cc_final: 0.8208 (t0) REVERT: E 237 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8212 (mt-10) outliers start: 11 outliers final: 5 residues processed: 240 average time/residue: 1.2532 time to fit residues: 338.0459 Evaluate side-chains 236 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 230 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.170410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.149469 restraints weight = 59449.235| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 0.77 r_work: 0.3356 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17995 Z= 0.121 Angle : 0.542 4.603 24520 Z= 0.278 Chirality : 0.039 0.151 2760 Planarity : 0.004 0.051 2890 Dihedral : 14.368 123.768 3930 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.72 % Allowed : 6.78 % Favored : 92.50 % 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: 1.17 (0.18), residues: 1970 helix: 1.75 (0.17), residues: 810 sheet: -0.31 (0.23), residues: 470 loop : 0.60 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 446 TYR 0.013 0.002 TYR A 273 PHE 0.010 0.001 PHE C 252 TRP 0.009 0.001 TRP D 307 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (17955) covalent geometry : angle 0.53091 / 0.28 (24410) SS BOND : bond 0.00737 / 0.40 ( 10) SS BOND : angle 1.32933 / 0.77 ( 20) hydrogen bonds : bond 0.04396 / 2.87 ( 861) hydrogen bonds : angle 4.87881 / 3.41 ( 2818) link_BETA1-4 : bond 0.00309 / 0.17 ( 15) link_BETA1-4 : angle 1.23890 / 0.88 ( 45) link_NAG-ASN : bond 0.00189 / 0.12 ( 15) link_NAG-ASN : angle 2.22807 / 1.47 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 231 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7981 (pt0) cc_final: 0.7716 (pt0) REVERT: A 156 ASP cc_start: 0.8433 (t0) cc_final: 0.8114 (t0) REVERT: B 98 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7195 (ptt90) REVERT: B 156 ASP cc_start: 0.8505 (t0) cc_final: 0.8220 (t0) REVERT: C 40 MET cc_start: 0.8420 (mtp) cc_final: 0.8188 (mtm) REVERT: C 428 ASP cc_start: 0.8037 (m-30) cc_final: 0.7830 (m-30) REVERT: D 156 ASP cc_start: 0.8380 (t0) cc_final: 0.8039 (t0) REVERT: D 450 MET cc_start: 0.8270 (mmp) cc_final: 0.7952 (ttt) REVERT: E 57 MET cc_start: 0.8706 (mtm) cc_final: 0.8461 (mtp) REVERT: E 156 ASP cc_start: 0.8394 (t0) cc_final: 0.8175 (t0) outliers start: 8 outliers final: 5 residues processed: 234 average time/residue: 1.2264 time to fit residues: 321.8005 Evaluate side-chains 234 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 9 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 104 optimal weight: 0.0470 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.169676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.149002 restraints weight = 56302.396| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 0.75 r_work: 0.3361 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17995 Z= 0.144 Angle : 0.572 5.265 24520 Z= 0.294 Chirality : 0.040 0.153 2760 Planarity : 0.004 0.046 2890 Dihedral : 14.366 120.659 3930 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.78 % Allowed : 6.89 % Favored : 92.33 % 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: 1.17 (0.18), residues: 1970 helix: 1.74 (0.17), residues: 810 sheet: -0.31 (0.23), residues: 475 loop : 0.64 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 446 TYR 0.014 0.002 TYR A 273 PHE 0.014 0.001 PHE E 99 TRP 0.009 0.001 TRP D 307 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (17955) covalent geometry : angle 0.56144 / 0.29 (24410) SS BOND : bond 0.00757 / 0.41 ( 10) SS BOND : angle 1.43822 / 0.83 ( 20) hydrogen bonds : bond 0.04718 / 3.08 ( 861) hydrogen bonds : angle 4.93770 / 3.45 ( 2818) link_BETA1-4 : bond 0.00285 / 0.16 ( 15) link_BETA1-4 : angle 1.26555 / 0.91 ( 45) link_NAG-ASN : bond 0.00239 / 0.15 ( 15) link_NAG-ASN : angle 2.17087 / 1.41 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 232 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7908 (tppp) REVERT: A 156 ASP cc_start: 0.8419 (t0) cc_final: 0.8170 (t0) REVERT: B 98 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7192 (ptt90) REVERT: B 156 ASP cc_start: 0.8532 (t0) cc_final: 0.8241 (t0) REVERT: C 12 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7929 (tppp) REVERT: C 40 MET cc_start: 0.8417 (mtp) cc_final: 0.8186 (mtm) REVERT: D 156 ASP cc_start: 0.8388 (t0) cc_final: 0.8078 (t0) REVERT: E 57 MET cc_start: 0.8718 (mtm) cc_final: 0.8440 (mtp) REVERT: E 237 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8185 (mt-10) outliers start: 9 outliers final: 5 residues processed: 236 average time/residue: 1.3313 time to fit residues: 353.4744 Evaluate side-chains 235 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 229 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 68 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 147 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.168200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.147007 restraints weight = 52240.486| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 0.76 r_work: 0.3336 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17995 Z= 0.182 Angle : 0.633 7.027 24520 Z= 0.326 Chirality : 0.042 0.171 2760 Planarity : 0.005 0.059 2890 Dihedral : 14.696 118.088 3930 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.78 % Allowed : 7.06 % Favored : 92.17 % 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: 0.97 (0.18), residues: 1970 helix: 1.55 (0.17), residues: 815 sheet: -0.38 (0.23), residues: 475 loop : 0.52 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 446 TYR 0.016 0.002 TYR A 273 PHE 0.020 0.002 PHE B 99 TRP 0.010 0.002 TRP A 148 HIS 0.006 0.002 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (17955) covalent geometry : angle 0.62209 / 0.32 (24410) SS BOND : bond 0.00809 / 0.43 ( 10) SS BOND : angle 1.61053 / 0.93 ( 20) hydrogen bonds : bond 0.05279 / 3.43 ( 861) hydrogen bonds : angle 5.12728 / 3.59 ( 2818) link_BETA1-4 : bond 0.00288 / 0.17 ( 15) link_BETA1-4 : angle 1.39734 / 1.01 ( 45) link_NAG-ASN : bond 0.00322 / 0.21 ( 15) link_NAG-ASN : angle 2.24729 / 1.44 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 236 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8291 (ttpt) cc_final: 0.8032 (tppp) REVERT: A 156 ASP cc_start: 0.8502 (t0) cc_final: 0.8206 (t0) REVERT: B 156 ASP cc_start: 0.8601 (t0) cc_final: 0.8281 (t0) REVERT: D 156 ASP cc_start: 0.8469 (t0) cc_final: 0.8115 (t0) REVERT: E 98 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7215 (ptt90) outliers start: 9 outliers final: 5 residues processed: 239 average time/residue: 1.4527 time to fit residues: 391.2739 Evaluate side-chains 238 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 232 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 30 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.167641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.146502 restraints weight = 53325.219| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 0.76 r_work: 0.3331 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17995 Z= 0.185 Angle : 0.634 5.808 24520 Z= 0.327 Chirality : 0.042 0.170 2760 Planarity : 0.005 0.055 2890 Dihedral : 14.723 116.369 3930 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.67 % Allowed : 7.22 % Favored : 92.11 % 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: 0.88 (0.18), residues: 1970 helix: 1.48 (0.17), residues: 815 sheet: -0.35 (0.23), residues: 480 loop : 0.40 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 446 TYR 0.017 0.002 TYR A 273 PHE 0.018 0.002 PHE E 99 TRP 0.009 0.002 TRP E 148 HIS 0.005 0.002 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (17955) covalent geometry : angle 0.62245 / 0.32 (24410) SS BOND : bond 0.00822 / 0.44 ( 10) SS BOND : angle 1.63630 / 0.95 ( 20) hydrogen bonds : bond 0.05241 / 3.41 ( 861) hydrogen bonds : angle 5.13310 / 3.60 ( 2818) link_BETA1-4 : bond 0.00292 / 0.17 ( 15) link_BETA1-4 : angle 1.41457 / 1.02 ( 45) link_NAG-ASN : bond 0.00311 / 0.20 ( 15) link_NAG-ASN : angle 2.30797 / 1.48 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 232 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8253 (ttpt) cc_final: 0.7987 (tppp) REVERT: B 98 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7235 (ptt90) REVERT: B 156 ASP cc_start: 0.8565 (t0) cc_final: 0.8273 (t0) REVERT: D 156 ASP cc_start: 0.8437 (t0) cc_final: 0.8101 (t0) REVERT: E 98 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7218 (ptt90) outliers start: 7 outliers final: 4 residues processed: 235 average time/residue: 1.4196 time to fit residues: 372.7966 Evaluate side-chains 239 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 233 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 88 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.170354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.149013 restraints weight = 52199.102| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 0.78 r_work: 0.3358 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17995 Z= 0.127 Angle : 0.551 5.289 24520 Z= 0.284 Chirality : 0.040 0.167 2760 Planarity : 0.004 0.045 2890 Dihedral : 14.137 111.468 3930 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.72 % Allowed : 7.22 % Favored : 92.06 % 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: 1.12 (0.18), residues: 1970 helix: 1.71 (0.17), residues: 810 sheet: -0.35 (0.23), residues: 475 loop : 0.60 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 446 TYR 0.015 0.002 TYR A 273 PHE 0.010 0.001 PHE B 99 TRP 0.008 0.001 TRP D 307 HIS 0.002 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (17955) covalent geometry : angle 0.53968 / 0.28 (24410) SS BOND : bond 0.00724 / 0.39 ( 10) SS BOND : angle 1.33302 / 0.77 ( 20) hydrogen bonds : bond 0.04487 / 2.93 ( 861) hydrogen bonds : angle 4.89745 / 3.43 ( 2818) link_BETA1-4 : bond 0.00289 / 0.15 ( 15) link_BETA1-4 : angle 1.28806 / 0.92 ( 45) link_NAG-ASN : bond 0.00206 / 0.14 ( 15) link_NAG-ASN : angle 2.27567 / 1.49 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12478.80 seconds wall clock time: 211 minutes 35.15 seconds (12695.15 seconds total)