Starting phenix.real_space_refine on Wed Mar 20 11:46:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhm_16060/03_2024/8bhm_16060_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhm_16060/03_2024/8bhm_16060.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhm_16060/03_2024/8bhm_16060_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhm_16060/03_2024/8bhm_16060_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhm_16060/03_2024/8bhm_16060_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhm_16060/03_2024/8bhm_16060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhm_16060/03_2024/8bhm_16060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhm_16060/03_2024/8bhm_16060_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhm_16060/03_2024/8bhm_16060_trim_updated.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 85 5.16 5 C 8920 2.51 5 N 2270 2.21 5 O 2490 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27180 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'R63': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'R63': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'R63': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'R63': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'R63': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.40, per 1000 atoms: 0.42 Number of scatterers: 27180 At special positions: 0 Unit cell: (94.01, 92.904, 123.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 O 2490 8.00 N 2270 7.00 C 8920 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 21.86 Conformation dependent library (CDL) restraints added in 2.8 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 20 sheets defined 36.6% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 234 through 249 removed outlier: 4.175A pdb=" N SER A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 279 removed outlier: 3.789A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 313 Processing helix chain 'A' and resid 318 through 417 removed outlier: 4.001A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 16 through 26 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 234 through 249 removed outlier: 4.176A pdb=" N SER B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 279 removed outlier: 3.788A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 313 Processing helix chain 'B' and resid 318 through 417 removed outlier: 4.001A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 16 through 26 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 178 through 181 No H-bonds generated for 'chain 'C' and resid 178 through 181' Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 234 through 249 removed outlier: 4.176A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 279 removed outlier: 3.789A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 313 Processing helix chain 'C' and resid 318 through 417 removed outlier: 4.001A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 16 through 26 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 178 through 181 No H-bonds generated for 'chain 'D' and resid 178 through 181' Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 234 through 249 removed outlier: 4.175A pdb=" N SER D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP D 249 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 279 removed outlier: 3.788A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 313 Processing helix chain 'D' and resid 318 through 417 removed outlier: 4.001A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 16 through 26 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 178 through 181 No H-bonds generated for 'chain 'E' and resid 178 through 181' Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 234 through 249 removed outlier: 4.176A pdb=" N SER E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 279 removed outlier: 3.789A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 313 Processing helix chain 'E' and resid 318 through 417 removed outlier: 4.002A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.831A pdb=" N THR A 42 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL A 173 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL A 44 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.653A pdb=" N MET A 48 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 102 through 104 Processing sheet with id= D, first strand: chain 'A' and resid 153 through 156 removed outlier: 3.844A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.831A pdb=" N THR B 42 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL B 173 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 44 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.653A pdb=" N MET B 48 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 102 through 104 Processing sheet with id= H, first strand: chain 'B' and resid 153 through 156 removed outlier: 3.844A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.831A pdb=" N THR C 42 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL C 173 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL C 44 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 182 through 184 removed outlier: 6.652A pdb=" N MET C 48 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 102 through 104 Processing sheet with id= L, first strand: chain 'C' and resid 153 through 156 removed outlier: 3.845A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.831A pdb=" N THR D 42 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL D 173 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL D 44 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 182 through 184 removed outlier: 6.653A pdb=" N MET D 48 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 102 through 104 Processing sheet with id= P, first strand: chain 'D' and resid 153 through 156 removed outlier: 3.844A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 170 through 174 removed outlier: 6.830A pdb=" N THR E 42 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL E 173 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL E 44 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.652A pdb=" N MET E 48 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 102 through 104 Processing sheet with id= T, first strand: chain 'E' and resid 153 through 156 removed outlier: 3.845A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1755 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: 9.95 Time building geometry restraints manager: 22.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 5 1.23 - 1.42: 6120 1.42 - 1.61: 7860 1.61 - 1.81: 150 Bond restraints: 27550 Sorted by residual: bond pdb=" N ASN E 14 " pdb=" H ASN E 14 " ideal model delta sigma weight residual 0.860 0.961 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N ASN D 14 " pdb=" H ASN D 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ASN B 14 " pdb=" H ASN B 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" N ASN C 14 " pdb=" H ASN C 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 27545 not shown) Histogram of bond angle deviations from ideal: 100.80 - 107.62: 1132 107.62 - 114.45: 32097 114.45 - 121.27: 10714 121.27 - 128.10: 5399 128.10 - 134.92: 173 Bond angle restraints: 49515 Sorted by residual: angle pdb=" C03 R63 D 502 " pdb=" C15 R63 D 502 " pdb=" C16 R63 D 502 " ideal model delta sigma weight residual 152.20 122.61 29.59 3.00e+00 1.11e-01 9.73e+01 angle pdb=" C03 R63 C 502 " pdb=" C15 R63 C 502 " pdb=" C16 R63 C 502 " ideal model delta sigma weight residual 152.20 122.62 29.58 3.00e+00 1.11e-01 9.72e+01 angle pdb=" C03 R63 A 502 " pdb=" C15 R63 A 502 " pdb=" C16 R63 A 502 " ideal model delta sigma weight residual 152.20 122.65 29.55 3.00e+00 1.11e-01 9.70e+01 angle pdb=" C03 R63 B 502 " pdb=" C15 R63 B 502 " pdb=" C16 R63 B 502 " ideal model delta sigma weight residual 152.20 122.66 29.54 3.00e+00 1.11e-01 9.70e+01 angle pdb=" C03 R63 E 502 " pdb=" C15 R63 E 502 " pdb=" C16 R63 E 502 " ideal model delta sigma weight residual 152.20 122.68 29.52 3.00e+00 1.11e-01 9.69e+01 ... (remaining 49510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 12595 14.62 - 29.24: 305 29.24 - 43.86: 95 43.86 - 58.48: 110 58.48 - 73.10: 10 Dihedral angle restraints: 13115 sinusoidal: 6985 harmonic: 6130 Sorted by residual: dihedral pdb=" C09 R63 D 502 " pdb=" C08 R63 D 502 " pdb=" O20 R63 D 502 " pdb=" C21 R63 D 502 " ideal model delta sinusoidal sigma weight residual -38.17 34.36 -72.53 1 3.00e+01 1.11e-03 7.46e+00 dihedral pdb=" C09 R63 E 502 " pdb=" C08 R63 E 502 " pdb=" O20 R63 E 502 " pdb=" C21 R63 E 502 " ideal model delta sinusoidal sigma weight residual -38.17 34.35 -72.52 1 3.00e+01 1.11e-03 7.46e+00 dihedral pdb=" C09 R63 B 502 " pdb=" C08 R63 B 502 " pdb=" O20 R63 B 502 " pdb=" C21 R63 B 502 " ideal model delta sinusoidal sigma weight residual -38.17 34.34 -72.51 1 3.00e+01 1.11e-03 7.46e+00 ... (remaining 13112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1271 0.024 - 0.048: 572 0.048 - 0.072: 161 0.072 - 0.096: 66 0.096 - 0.121: 90 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE C 41 " pdb=" N ILE C 41 " pdb=" C ILE C 41 " pdb=" CB ILE C 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ILE B 41 " pdb=" N ILE B 41 " pdb=" C ILE B 41 " pdb=" CB ILE B 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 2157 not shown) Planarity restraints: 3990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 R63 C 502 " -0.002 2.00e-02 2.50e+03 1.10e-02 5.18e+00 pdb=" C03 R63 C 502 " 0.003 2.00e-02 2.50e+03 pdb=" C04 R63 C 502 " 0.010 2.00e-02 2.50e+03 pdb=" C05 R63 C 502 " 0.010 2.00e-02 2.50e+03 pdb=" C06 R63 C 502 " 0.010 2.00e-02 2.50e+03 pdb=" C07 R63 C 502 " 0.004 2.00e-02 2.50e+03 pdb=" C08 R63 C 502 " -0.006 2.00e-02 2.50e+03 pdb=" C09 R63 C 502 " -0.001 2.00e-02 2.50e+03 pdb=" C10 R63 C 502 " 0.006 2.00e-02 2.50e+03 pdb=" C12 R63 C 502 " 0.008 2.00e-02 2.50e+03 pdb=" C13 R63 C 502 " 0.001 2.00e-02 2.50e+03 pdb=" C15 R63 C 502 " -0.005 2.00e-02 2.50e+03 pdb=" C16 R63 C 502 " -0.019 2.00e-02 2.50e+03 pdb=" N11 R63 C 502 " 0.007 2.00e-02 2.50e+03 pdb=" N14 R63 C 502 " -0.005 2.00e-02 2.50e+03 pdb=" O20 R63 C 502 " -0.032 2.00e-02 2.50e+03 pdb=" O22 R63 C 502 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 R63 A 502 " 0.002 2.00e-02 2.50e+03 1.10e-02 5.12e+00 pdb=" C03 R63 A 502 " -0.004 2.00e-02 2.50e+03 pdb=" C04 R63 A 502 " -0.010 2.00e-02 2.50e+03 pdb=" C05 R63 A 502 " -0.010 2.00e-02 2.50e+03 pdb=" C06 R63 A 502 " -0.010 2.00e-02 2.50e+03 pdb=" C07 R63 A 502 " -0.003 2.00e-02 2.50e+03 pdb=" C08 R63 A 502 " 0.006 2.00e-02 2.50e+03 pdb=" C09 R63 A 502 " 0.002 2.00e-02 2.50e+03 pdb=" C10 R63 A 502 " -0.007 2.00e-02 2.50e+03 pdb=" C12 R63 A 502 " -0.008 2.00e-02 2.50e+03 pdb=" C13 R63 A 502 " -0.001 2.00e-02 2.50e+03 pdb=" C15 R63 A 502 " 0.005 2.00e-02 2.50e+03 pdb=" C16 R63 A 502 " 0.019 2.00e-02 2.50e+03 pdb=" N11 R63 A 502 " -0.007 2.00e-02 2.50e+03 pdb=" N14 R63 A 502 " 0.005 2.00e-02 2.50e+03 pdb=" O20 R63 A 502 " 0.032 2.00e-02 2.50e+03 pdb=" O22 R63 A 502 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 R63 E 502 " 0.002 2.00e-02 2.50e+03 1.10e-02 5.11e+00 pdb=" C03 R63 E 502 " -0.003 2.00e-02 2.50e+03 pdb=" C04 R63 E 502 " -0.010 2.00e-02 2.50e+03 pdb=" C05 R63 E 502 " -0.010 2.00e-02 2.50e+03 pdb=" C06 R63 E 502 " -0.010 2.00e-02 2.50e+03 pdb=" C07 R63 E 502 " -0.004 2.00e-02 2.50e+03 pdb=" C08 R63 E 502 " 0.006 2.00e-02 2.50e+03 pdb=" C09 R63 E 502 " 0.001 2.00e-02 2.50e+03 pdb=" C10 R63 E 502 " -0.006 2.00e-02 2.50e+03 pdb=" C12 R63 E 502 " -0.007 2.00e-02 2.50e+03 pdb=" C13 R63 E 502 " -0.002 2.00e-02 2.50e+03 pdb=" C15 R63 E 502 " 0.004 2.00e-02 2.50e+03 pdb=" C16 R63 E 502 " 0.019 2.00e-02 2.50e+03 pdb=" N11 R63 E 502 " -0.007 2.00e-02 2.50e+03 pdb=" N14 R63 E 502 " 0.005 2.00e-02 2.50e+03 pdb=" O20 R63 E 502 " 0.032 2.00e-02 2.50e+03 pdb=" O22 R63 E 502 " -0.010 2.00e-02 2.50e+03 ... (remaining 3987 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 2995 2.26 - 2.85: 62216 2.85 - 3.43: 68434 3.43 - 4.02: 98166 4.02 - 4.60: 149676 Nonbonded interactions: 381487 Sorted by model distance: nonbonded pdb=" H ASN D 167 " pdb=" O GLU D 212 " model vdw 1.677 1.850 nonbonded pdb=" H ASN A 167 " pdb=" O GLU A 212 " model vdw 1.677 1.850 nonbonded pdb=" H ASN C 167 " pdb=" O GLU C 212 " model vdw 1.677 1.850 nonbonded pdb=" H ASN E 167 " pdb=" O GLU E 212 " model vdw 1.678 1.850 nonbonded pdb=" H ASN B 167 " pdb=" O GLU B 212 " model vdw 1.678 1.850 ... (remaining 381482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.300 Extract box with map and model: 6.590 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 84.890 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.130 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 : 0.003 0.067 14135 Z= 0.219 Angle : 0.908 29.589 19240 Z= 0.326 Chirality : 0.037 0.121 2160 Planarity : 0.003 0.024 2385 Dihedral : 6.752 73.098 5105 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.22), residues: 1670 helix: 3.28 (0.22), residues: 585 sheet: 0.80 (0.27), residues: 435 loop : 0.74 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 73 HIS 0.002 0.000 HIS D 195 PHE 0.003 0.000 PHE C 149 TYR 0.004 0.001 TYR D 285 ARG 0.001 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 CYS cc_start: 0.9496 (m) cc_final: 0.9210 (m) REVERT: A 289 MET cc_start: 0.9160 (ttp) cc_final: 0.8935 (ttm) REVERT: B 197 MET cc_start: 0.9212 (mmm) cc_final: 0.9003 (mmp) REVERT: B 237 CYS cc_start: 0.9465 (m) cc_final: 0.9204 (m) REVERT: C 197 MET cc_start: 0.9220 (mmm) cc_final: 0.8962 (mmm) REVERT: C 289 MET cc_start: 0.9151 (ttp) cc_final: 0.8919 (ttm) REVERT: D 289 MET cc_start: 0.9123 (ttp) cc_final: 0.8911 (ttm) REVERT: E 289 MET cc_start: 0.9149 (ttp) cc_final: 0.8933 (ttm) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 2.7577 time to fit residues: 437.5125 Evaluate side-chains 111 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0370 chunk 125 optimal weight: 0.0370 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14135 Z= 0.171 Angle : 0.473 6.172 19240 Z= 0.240 Chirality : 0.039 0.131 2160 Planarity : 0.004 0.063 2385 Dihedral : 4.406 47.100 1970 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.21 % Allowed : 5.10 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.21), residues: 1670 helix: 3.34 (0.22), residues: 575 sheet: 1.18 (0.29), residues: 385 loop : 0.37 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 114 HIS 0.003 0.001 HIS E 113 PHE 0.007 0.001 PHE C 409 TYR 0.008 0.001 TYR A 413 ARG 0.004 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 MET cc_start: 0.9211 (mmm) cc_final: 0.8920 (mmm) REVERT: C 289 MET cc_start: 0.8950 (ttp) cc_final: 0.8750 (ttm) REVERT: E 289 MET cc_start: 0.9004 (ttp) cc_final: 0.8797 (ttm) outliers start: 18 outliers final: 9 residues processed: 126 average time/residue: 2.4704 time to fit residues: 346.6783 Evaluate side-chains 118 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14135 Z= 0.319 Angle : 0.520 7.719 19240 Z= 0.268 Chirality : 0.040 0.132 2160 Planarity : 0.004 0.039 2385 Dihedral : 4.645 48.110 1970 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.14 % Allowed : 4.90 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.21), residues: 1670 helix: 3.12 (0.22), residues: 580 sheet: 0.83 (0.28), residues: 410 loop : 0.36 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 114 HIS 0.004 0.001 HIS D 105 PHE 0.011 0.001 PHE A 307 TYR 0.012 0.001 TYR B 132 ARG 0.004 0.001 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.9329 (ttm) cc_final: 0.9081 (ttm) REVERT: B 115 MET cc_start: 0.8947 (mmp) cc_final: 0.8729 (mmp) REVERT: C 289 MET cc_start: 0.9158 (ttp) cc_final: 0.8922 (ttm) REVERT: D 216 MET cc_start: 0.9108 (mmm) cc_final: 0.8765 (mmm) REVERT: D 289 MET cc_start: 0.9129 (ttp) cc_final: 0.8881 (ttm) REVERT: E 289 MET cc_start: 0.9185 (ttp) cc_final: 0.8919 (ttm) outliers start: 17 outliers final: 10 residues processed: 114 average time/residue: 2.3887 time to fit residues: 303.4800 Evaluate side-chains 114 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.9980 chunk 112 optimal weight: 0.0000 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14135 Z= 0.218 Angle : 0.461 8.726 19240 Z= 0.233 Chirality : 0.039 0.121 2160 Planarity : 0.004 0.039 2385 Dihedral : 4.309 43.717 1970 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.74 % Allowed : 5.91 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.21), residues: 1670 helix: 3.21 (0.22), residues: 580 sheet: 0.95 (0.29), residues: 385 loop : 0.38 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 114 HIS 0.003 0.001 HIS E 105 PHE 0.008 0.001 PHE E 261 TYR 0.009 0.001 TYR E 297 ARG 0.003 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.9324 (ttm) cc_final: 0.9051 (ttm) REVERT: C 216 MET cc_start: 0.8865 (mmm) cc_final: 0.8279 (mmm) REVERT: C 289 MET cc_start: 0.9188 (ttp) cc_final: 0.8927 (ttm) REVERT: D 216 MET cc_start: 0.9089 (mmm) cc_final: 0.8784 (mmm) REVERT: D 289 MET cc_start: 0.9145 (ttp) cc_final: 0.8847 (ttm) REVERT: E 289 MET cc_start: 0.9176 (ttp) cc_final: 0.8900 (ttm) outliers start: 11 outliers final: 8 residues processed: 109 average time/residue: 2.4320 time to fit residues: 294.8906 Evaluate side-chains 112 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14135 Z= 0.248 Angle : 0.471 8.713 19240 Z= 0.238 Chirality : 0.039 0.121 2160 Planarity : 0.004 0.039 2385 Dihedral : 4.303 41.654 1970 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.67 % Allowed : 6.17 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.21), residues: 1670 helix: 3.22 (0.21), residues: 580 sheet: 0.74 (0.28), residues: 410 loop : 0.36 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 114 HIS 0.004 0.001 HIS B 195 PHE 0.008 0.001 PHE A 307 TYR 0.009 0.001 TYR E 297 ARG 0.001 0.000 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.9348 (ttm) cc_final: 0.9060 (ttm) REVERT: C 289 MET cc_start: 0.9224 (ttp) cc_final: 0.8993 (ttm) REVERT: D 289 MET cc_start: 0.9182 (ttp) cc_final: 0.8931 (ttm) REVERT: E 61 MET cc_start: 0.9431 (mtp) cc_final: 0.9111 (mmm) REVERT: E 289 MET cc_start: 0.9206 (ttp) cc_final: 0.8942 (ttm) outliers start: 10 outliers final: 9 residues processed: 110 average time/residue: 2.5005 time to fit residues: 311.0062 Evaluate side-chains 107 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 14135 Z= 0.447 Angle : 0.547 9.847 19240 Z= 0.284 Chirality : 0.040 0.128 2160 Planarity : 0.004 0.042 2385 Dihedral : 4.696 40.113 1970 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.87 % Allowed : 6.64 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.21), residues: 1670 helix: 2.99 (0.21), residues: 580 sheet: 0.37 (0.27), residues: 415 loop : 0.18 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 249 HIS 0.005 0.001 HIS D 105 PHE 0.012 0.001 PHE A 307 TYR 0.011 0.001 TYR E 413 ARG 0.003 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.9399 (ttm) cc_final: 0.9150 (ttm) REVERT: C 289 MET cc_start: 0.9291 (ttp) cc_final: 0.9035 (ttm) REVERT: D 289 MET cc_start: 0.9224 (ttp) cc_final: 0.8993 (ttm) REVERT: E 280 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8319 (tm) REVERT: E 289 MET cc_start: 0.9283 (ttp) cc_final: 0.9010 (ttm) outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 2.3265 time to fit residues: 273.0240 Evaluate side-chains 108 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14135 Z= 0.299 Angle : 0.502 9.751 19240 Z= 0.254 Chirality : 0.039 0.144 2160 Planarity : 0.004 0.043 2385 Dihedral : 4.454 37.840 1970 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.74 % Allowed : 7.58 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.21), residues: 1670 helix: 3.16 (0.22), residues: 580 sheet: 0.38 (0.27), residues: 410 loop : 0.22 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 114 HIS 0.004 0.001 HIS E 105 PHE 0.009 0.001 PHE A 301 TYR 0.008 0.001 TYR B 413 ARG 0.001 0.000 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.9378 (ttm) cc_final: 0.9135 (ttm) REVERT: C 289 MET cc_start: 0.9270 (ttp) cc_final: 0.8991 (ttm) REVERT: D 289 MET cc_start: 0.9230 (ttp) cc_final: 0.9024 (ttp) REVERT: E 289 MET cc_start: 0.9271 (ttp) cc_final: 0.8989 (ttm) outliers start: 11 outliers final: 8 residues processed: 104 average time/residue: 2.3684 time to fit residues: 274.4919 Evaluate side-chains 107 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14135 Z= 0.169 Angle : 0.474 8.271 19240 Z= 0.234 Chirality : 0.039 0.158 2160 Planarity : 0.004 0.043 2385 Dihedral : 4.161 38.226 1970 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.67 % Allowed : 7.45 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.21), residues: 1670 helix: 3.48 (0.22), residues: 575 sheet: 0.63 (0.28), residues: 385 loop : 0.26 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 114 HIS 0.002 0.001 HIS E 105 PHE 0.008 0.001 PHE A 301 TYR 0.007 0.001 TYR E 413 ARG 0.001 0.000 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.9358 (ttm) cc_final: 0.9092 (ttm) REVERT: C 289 MET cc_start: 0.9244 (ttp) cc_final: 0.8961 (ttm) REVERT: D 289 MET cc_start: 0.9165 (ttp) cc_final: 0.8944 (ttp) REVERT: E 289 MET cc_start: 0.9232 (ttp) cc_final: 0.8944 (ttm) outliers start: 10 outliers final: 8 residues processed: 106 average time/residue: 2.4615 time to fit residues: 290.8524 Evaluate side-chains 108 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 148 optimal weight: 0.0370 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14135 Z= 0.195 Angle : 0.482 7.784 19240 Z= 0.238 Chirality : 0.038 0.182 2160 Planarity : 0.004 0.043 2385 Dihedral : 4.095 37.175 1970 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.60 % Allowed : 7.79 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.21), residues: 1670 helix: 3.53 (0.21), residues: 575 sheet: 0.62 (0.28), residues: 385 loop : 0.21 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 114 HIS 0.003 0.001 HIS E 105 PHE 0.007 0.001 PHE A 301 TYR 0.012 0.001 TYR E 297 ARG 0.001 0.000 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.9365 (ttm) cc_final: 0.9104 (ttm) REVERT: C 62 GLU cc_start: 0.8999 (pp20) cc_final: 0.8658 (pp20) REVERT: C 289 MET cc_start: 0.9248 (ttp) cc_final: 0.8971 (ttm) REVERT: D 289 MET cc_start: 0.9165 (ttp) cc_final: 0.8945 (ttp) REVERT: E 289 MET cc_start: 0.9241 (ttp) cc_final: 0.8955 (ttm) outliers start: 9 outliers final: 9 residues processed: 107 average time/residue: 2.4236 time to fit residues: 290.3243 Evaluate side-chains 110 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 164 optimal weight: 0.0270 chunk 151 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14135 Z= 0.153 Angle : 0.495 10.263 19240 Z= 0.239 Chirality : 0.038 0.136 2160 Planarity : 0.004 0.043 2385 Dihedral : 3.972 37.763 1970 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.54 % Allowed : 8.12 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.21), residues: 1670 helix: 3.65 (0.21), residues: 575 sheet: 0.66 (0.28), residues: 385 loop : 0.25 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 114 HIS 0.002 0.001 HIS D 105 PHE 0.007 0.001 PHE A 301 TYR 0.010 0.001 TYR B 297 ARG 0.001 0.000 ARG C 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 GLU cc_start: 0.8952 (pp20) cc_final: 0.8606 (pp20) REVERT: C 289 MET cc_start: 0.9216 (ttp) cc_final: 0.8930 (ttm) REVERT: D 289 MET cc_start: 0.9155 (ttp) cc_final: 0.8933 (ttp) REVERT: E 289 MET cc_start: 0.9224 (ttp) cc_final: 0.8938 (ttm) REVERT: E 302 SER cc_start: 0.9562 (m) cc_final: 0.9307 (p) outliers start: 8 outliers final: 7 residues processed: 108 average time/residue: 2.3804 time to fit residues: 287.4720 Evaluate side-chains 111 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 16 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.054964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.046326 restraints weight = 127458.844| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.35 r_work: 0.2539 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14135 Z= 0.146 Angle : 0.488 9.371 19240 Z= 0.236 Chirality : 0.038 0.120 2160 Planarity : 0.004 0.042 2385 Dihedral : 3.836 37.348 1970 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.54 % Allowed : 8.12 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.22), residues: 1670 helix: 3.76 (0.22), residues: 575 sheet: 0.79 (0.29), residues: 380 loop : 0.21 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 114 HIS 0.002 0.001 HIS D 195 PHE 0.007 0.001 PHE E 261 TYR 0.010 0.001 TYR E 297 ARG 0.001 0.000 ARG C 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6785.96 seconds wall clock time: 120 minutes 13.31 seconds (7213.31 seconds total)