Starting phenix.real_space_refine on Wed Mar 20 12:01:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhb_16051/03_2024/8bhb_16051_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhb_16051/03_2024/8bhb_16051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhb_16051/03_2024/8bhb_16051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhb_16051/03_2024/8bhb_16051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhb_16051/03_2024/8bhb_16051_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhb_16051/03_2024/8bhb_16051_trim_updated.pdb" } resolution = 2.54 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= 0.009 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 8910 2.51 5 N 2290 2.21 5 O 2550 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: 27250 Number of models: 1 Model: "" Number of chains: 15 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'EIE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'EIE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'EIE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'EIE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'EIE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 12.75, per 1000 atoms: 0.47 Number of scatterers: 27250 At special positions: 0 Unit cell: (90.628, 93.888, 123.228, 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 2550 8.00 N 2290 7.00 C 8910 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: 23.30 Conformation dependent library (CDL) restraints added in 3.0 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 36.3% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.30 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: 4.150A pdb=" N SER A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TRP A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 279 removed outlier: 4.147A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 312 Processing helix chain 'A' and resid 318 through 417 removed outlier: 4.033A 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: 4.150A pdb=" N SER B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TRP B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 279 removed outlier: 4.147A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 312 Processing helix chain 'B' and resid 318 through 417 removed outlier: 4.033A 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: 4.150A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TRP C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 279 removed outlier: 4.148A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 312 Processing helix chain 'C' and resid 318 through 417 removed outlier: 4.033A 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: 4.150A pdb=" N SER D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TRP D 249 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 279 removed outlier: 4.147A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 312 Processing helix chain 'D' and resid 318 through 417 removed outlier: 4.034A 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: 4.149A pdb=" N SER E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TRP E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 279 removed outlier: 4.147A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 312 Processing helix chain 'E' and resid 318 through 417 removed outlier: 4.033A 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: 6.560A pdb=" N THR A 42 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL A 173 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL A 44 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 48 through 50 Processing sheet with id= C, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 107 through 112 removed outlier: 7.067A pdb=" N SER A 139 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER A 110 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR A 137 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.560A pdb=" N THR B 42 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL B 173 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL B 44 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 48 through 50 Processing sheet with id= G, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 107 through 112 removed outlier: 7.067A pdb=" N SER B 139 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER B 110 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR B 137 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.561A pdb=" N THR C 42 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL C 173 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL C 44 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 48 through 50 Processing sheet with id= K, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 107 through 112 removed outlier: 7.068A pdb=" N SER C 139 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER C 110 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C 137 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.560A pdb=" N THR D 42 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL D 173 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL D 44 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 48 through 50 Processing sheet with id= O, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 107 through 112 removed outlier: 7.068A pdb=" N SER D 139 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER D 110 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR D 137 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 170 through 174 removed outlier: 6.561A pdb=" N THR E 42 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL E 173 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL E 44 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 48 through 50 Processing sheet with id= S, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 107 through 112 removed outlier: 7.067A pdb=" N SER E 139 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER E 110 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR E 137 " --> pdb=" O SER E 110 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1890 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: 11.09 Time building geometry restraints manager: 24.30 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: 18 1.23 - 1.42: 6102 1.42 - 1.62: 7870 1.62 - 1.81: 150 Bond restraints: 27555 Sorted by residual: bond pdb=" N ASN B 14 " pdb=" H ASN B 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.49e+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 2.48e+01 bond pdb=" N ASN E 14 " pdb=" H ASN E 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN C 14 " pdb=" H ASN C 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 27550 not shown) Histogram of bond angle deviations from ideal: 100.34 - 114.23: 33060 114.23 - 128.13: 16295 128.13 - 142.02: 160 142.02 - 155.92: 0 155.92 - 169.81: 5 Bond angle restraints: 49520 Sorted by residual: angle pdb=" C MET D 115 " pdb=" N THR D 116 " pdb=" CA THR D 116 " ideal model delta sigma weight residual 121.70 126.91 -5.21 1.80e+00 3.09e-01 8.37e+00 angle pdb=" C MET C 115 " pdb=" N THR C 116 " pdb=" CA THR C 116 " ideal model delta sigma weight residual 121.70 126.87 -5.17 1.80e+00 3.09e-01 8.26e+00 angle pdb=" C MET B 115 " pdb=" N THR B 116 " pdb=" CA THR B 116 " ideal model delta sigma weight residual 121.70 126.86 -5.16 1.80e+00 3.09e-01 8.22e+00 angle pdb=" C MET E 115 " pdb=" N THR E 116 " pdb=" CA THR E 116 " ideal model delta sigma weight residual 121.70 126.85 -5.15 1.80e+00 3.09e-01 8.20e+00 angle pdb=" C MET A 115 " pdb=" N THR A 116 " pdb=" CA THR A 116 " ideal model delta sigma weight residual 121.70 126.83 -5.13 1.80e+00 3.09e-01 8.12e+00 ... (remaining 49515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 12603 15.91 - 31.82: 382 31.82 - 47.73: 90 47.73 - 63.63: 95 63.63 - 79.54: 5 Dihedral angle restraints: 13175 sinusoidal: 7045 harmonic: 6130 Sorted by residual: dihedral pdb=" CB MET E 115 " pdb=" CG MET E 115 " pdb=" SD MET E 115 " pdb=" CE MET E 115 " ideal model delta sinusoidal sigma weight residual 60.00 103.42 -43.42 3 1.50e+01 4.44e-03 7.80e+00 dihedral pdb=" CB MET D 115 " pdb=" CG MET D 115 " pdb=" SD MET D 115 " pdb=" CE MET D 115 " ideal model delta sinusoidal sigma weight residual 60.00 103.41 -43.41 3 1.50e+01 4.44e-03 7.80e+00 dihedral pdb=" CB MET A 115 " pdb=" CG MET A 115 " pdb=" SD MET A 115 " pdb=" CE MET A 115 " ideal model delta sinusoidal sigma weight residual 60.00 103.40 -43.40 3 1.50e+01 4.44e-03 7.80e+00 ... (remaining 13172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1225 0.024 - 0.047: 607 0.047 - 0.071: 173 0.071 - 0.095: 71 0.095 - 0.119: 84 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE D 124 " pdb=" N ILE D 124 " pdb=" C ILE D 124 " pdb=" CB ILE D 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA ILE E 124 " pdb=" N ILE E 124 " pdb=" C ILE E 124 " pdb=" CB ILE E 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 2157 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 EIE E 502 " 0.482 2.00e-02 2.50e+03 4.61e-01 5.84e+03 pdb=" C11 EIE E 502 " 0.364 2.00e-02 2.50e+03 pdb=" C12 EIE E 502 " 0.062 2.00e-02 2.50e+03 pdb=" C13 EIE E 502 " -0.130 2.00e-02 2.50e+03 pdb=" C7 EIE E 502 " -0.210 2.00e-02 2.50e+03 pdb=" C8 EIE E 502 " -0.015 2.00e-02 2.50e+03 pdb=" C9 EIE E 502 " 0.294 2.00e-02 2.50e+03 pdb=" N1 EIE E 502 " 0.787 2.00e-02 2.50e+03 pdb=" N2 EIE E 502 " -0.210 2.00e-02 2.50e+03 pdb=" N3 EIE E 502 " -0.978 2.00e-02 2.50e+03 pdb=" N4 EIE E 502 " -0.445 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 EIE D 502 " -0.482 2.00e-02 2.50e+03 4.61e-01 5.84e+03 pdb=" C11 EIE D 502 " -0.364 2.00e-02 2.50e+03 pdb=" C12 EIE D 502 " -0.062 2.00e-02 2.50e+03 pdb=" C13 EIE D 502 " 0.131 2.00e-02 2.50e+03 pdb=" C7 EIE D 502 " 0.210 2.00e-02 2.50e+03 pdb=" C8 EIE D 502 " 0.014 2.00e-02 2.50e+03 pdb=" C9 EIE D 502 " -0.294 2.00e-02 2.50e+03 pdb=" N1 EIE D 502 " -0.787 2.00e-02 2.50e+03 pdb=" N2 EIE D 502 " 0.211 2.00e-02 2.50e+03 pdb=" N3 EIE D 502 " 0.978 2.00e-02 2.50e+03 pdb=" N4 EIE D 502 " 0.445 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 EIE B 502 " -0.482 2.00e-02 2.50e+03 4.61e-01 5.83e+03 pdb=" C11 EIE B 502 " -0.365 2.00e-02 2.50e+03 pdb=" C12 EIE B 502 " -0.062 2.00e-02 2.50e+03 pdb=" C13 EIE B 502 " 0.130 2.00e-02 2.50e+03 pdb=" C7 EIE B 502 " 0.209 2.00e-02 2.50e+03 pdb=" C8 EIE B 502 " 0.015 2.00e-02 2.50e+03 pdb=" C9 EIE B 502 " -0.294 2.00e-02 2.50e+03 pdb=" N1 EIE B 502 " -0.787 2.00e-02 2.50e+03 pdb=" N2 EIE B 502 " 0.211 2.00e-02 2.50e+03 pdb=" N3 EIE B 502 " 0.978 2.00e-02 2.50e+03 pdb=" N4 EIE B 502 " 0.445 2.00e-02 2.50e+03 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 2420 2.25 - 2.83: 62120 2.83 - 3.42: 69984 3.42 - 4.01: 100703 4.01 - 4.60: 155292 Nonbonded interactions: 390519 Sorted by model distance: nonbonded pdb=" H ASN A 167 " pdb=" O GLU A 212 " model vdw 1.657 1.850 nonbonded pdb=" H ASN E 167 " pdb=" O GLU E 212 " model vdw 1.657 1.850 nonbonded pdb=" H ASN B 167 " pdb=" O GLU B 212 " model vdw 1.658 1.850 nonbonded pdb=" H ASN C 167 " pdb=" O GLU C 212 " model vdw 1.658 1.850 nonbonded pdb=" H ASN D 167 " pdb=" O GLU D 212 " model vdw 1.658 1.850 ... (remaining 390514 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: 8.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.440 Extract box with map and model: 30.020 Check model and map are aligned: 0.390 Set scattering table: 0.290 Process input model: 92.030 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 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 0.050 14140 Z= 0.169 Angle : 0.415 6.270 19245 Z= 0.193 Chirality : 0.037 0.119 2160 Planarity : 0.021 0.461 2395 Dihedral : 7.198 79.543 5165 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.09 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: 2.13 (0.21), residues: 1670 helix: 2.96 (0.22), residues: 585 sheet: 0.65 (0.27), residues: 435 loop : 0.61 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 414 HIS 0.003 0.001 HIS B 195 PHE 0.005 0.001 PHE E 104 TYR 0.005 0.001 TYR B 285 ARG 0.001 0.000 ARG A 320 *********************** 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 265 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.048 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: A 109 LYS cc_start: 0.8597 (tttt) cc_final: 0.8284 (tptp) REVERT: A 193 GLN cc_start: 0.8146 (pt0) cc_final: 0.7829 (pm20) REVERT: B 109 LYS cc_start: 0.8583 (tttt) cc_final: 0.8245 (tptp) REVERT: B 193 GLN cc_start: 0.8164 (pt0) cc_final: 0.7957 (pm20) REVERT: B 253 GLU cc_start: 0.8677 (pm20) cc_final: 0.7852 (pm20) REVERT: C 109 LYS cc_start: 0.8597 (tttt) cc_final: 0.8272 (tptp) REVERT: D 109 LYS cc_start: 0.8619 (tttt) cc_final: 0.8304 (tptp) REVERT: D 193 GLN cc_start: 0.8169 (pt0) cc_final: 0.7950 (pm20) REVERT: E 109 LYS cc_start: 0.8603 (tttt) cc_final: 0.8289 (tptp) REVERT: E 193 GLN cc_start: 0.8149 (pt0) cc_final: 0.7898 (pm20) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 3.2391 time to fit residues: 927.1447 Evaluate side-chains 135 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 2.241 ------------------------------------------------------------------------------- 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: 0.0670 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 155 ASN C 155 ASN D 155 ASN E 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14140 Z= 0.231 Angle : 0.487 7.121 19245 Z= 0.256 Chirality : 0.041 0.133 2160 Planarity : 0.004 0.031 2395 Dihedral : 3.701 18.636 2030 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.81 % Allowed : 6.38 % Favored : 91.81 % 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: 2.12 (0.21), residues: 1670 helix: 3.13 (0.21), residues: 580 sheet: 0.67 (0.25), residues: 455 loop : 0.41 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 291 HIS 0.003 0.001 HIS C 221 PHE 0.012 0.002 PHE D 68 TYR 0.008 0.001 TYR E 413 ARG 0.002 0.000 ARG A 123 *********************** 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 180 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 2.120 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 109 LYS cc_start: 0.8603 (tttt) cc_final: 0.8276 (tptp) REVERT: A 193 GLN cc_start: 0.8214 (pt0) cc_final: 0.7885 (pm20) REVERT: B 109 LYS cc_start: 0.8591 (tttt) cc_final: 0.8259 (tptp) REVERT: B 115 MET cc_start: 0.8508 (mmp) cc_final: 0.7961 (mmp) REVERT: B 193 GLN cc_start: 0.8203 (pt0) cc_final: 0.7967 (pm20) REVERT: B 251 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7409 (t0) REVERT: C 109 LYS cc_start: 0.8580 (tttt) cc_final: 0.8235 (tptp) REVERT: C 277 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7777 (mmt180) REVERT: D 109 LYS cc_start: 0.8629 (tttt) cc_final: 0.8288 (tptp) REVERT: D 193 GLN cc_start: 0.8257 (pt0) cc_final: 0.7998 (pm20) REVERT: D 251 ASN cc_start: 0.8064 (t0) cc_final: 0.7702 (t0) REVERT: E 109 LYS cc_start: 0.8605 (tttt) cc_final: 0.8290 (tptp) REVERT: E 193 GLN cc_start: 0.8200 (pt0) cc_final: 0.7931 (pm20) outliers start: 27 outliers final: 11 residues processed: 162 average time/residue: 2.5907 time to fit residues: 463.5353 Evaluate side-chains 142 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 2.249 ------------------------------------------------------------------------------- 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 251 ASN 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 D residue 47 ASP Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.0870 chunk 124 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14140 Z= 0.229 Angle : 0.464 6.324 19245 Z= 0.243 Chirality : 0.040 0.125 2160 Planarity : 0.004 0.034 2395 Dihedral : 3.860 17.760 2030 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.08 % Allowed : 6.38 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.06 (0.21), residues: 1670 helix: 3.16 (0.22), residues: 580 sheet: 0.56 (0.25), residues: 455 loop : 0.34 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 414 HIS 0.004 0.001 HIS E 221 PHE 0.012 0.001 PHE E 68 TYR 0.011 0.001 TYR A 132 ARG 0.002 0.000 ARG C 320 *********************** 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 176 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 2.145 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: A 109 LYS cc_start: 0.8591 (tttt) cc_final: 0.8242 (tptp) REVERT: A 147 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7967 (tp30) REVERT: A 193 GLN cc_start: 0.8257 (pt0) cc_final: 0.7964 (pm20) REVERT: B 109 LYS cc_start: 0.8563 (tttt) cc_final: 0.8201 (tptp) REVERT: B 193 GLN cc_start: 0.8222 (pt0) cc_final: 0.7984 (pm20) REVERT: C 60 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8175 (mt-10) REVERT: C 109 LYS cc_start: 0.8570 (tttt) cc_final: 0.8219 (tptp) REVERT: D 109 LYS cc_start: 0.8588 (tttt) cc_final: 0.8221 (tptp) REVERT: D 193 GLN cc_start: 0.8288 (pt0) cc_final: 0.8017 (pm20) REVERT: D 251 ASN cc_start: 0.8081 (t0) cc_final: 0.7729 (t0) REVERT: D 395 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8366 (m-30) REVERT: E 109 LYS cc_start: 0.8577 (tttt) cc_final: 0.8223 (tptp) REVERT: E 193 GLN cc_start: 0.8234 (pt0) cc_final: 0.7938 (pm20) outliers start: 31 outliers final: 9 residues processed: 157 average time/residue: 2.3244 time to fit residues: 407.5873 Evaluate side-chains 142 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 395 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.1980 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14140 Z= 0.217 Angle : 0.451 6.122 19245 Z= 0.234 Chirality : 0.039 0.123 2160 Planarity : 0.004 0.035 2395 Dihedral : 3.917 18.737 2030 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.74 % Allowed : 6.98 % Favored : 91.28 % 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: 2.01 (0.21), residues: 1670 helix: 3.16 (0.21), residues: 580 sheet: 0.46 (0.25), residues: 455 loop : 0.32 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 73 HIS 0.003 0.001 HIS C 221 PHE 0.009 0.001 PHE A 104 TYR 0.008 0.001 TYR A 132 ARG 0.001 0.000 ARG D 123 *********************** 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 165 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 2.376 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: A 109 LYS cc_start: 0.8550 (tttt) cc_final: 0.8197 (tptp) REVERT: A 193 GLN cc_start: 0.8260 (pt0) cc_final: 0.7960 (pm20) REVERT: B 109 LYS cc_start: 0.8526 (tttt) cc_final: 0.8160 (tptp) REVERT: B 134 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8967 (pt) REVERT: B 193 GLN cc_start: 0.8225 (pt0) cc_final: 0.7977 (pm20) REVERT: C 109 LYS cc_start: 0.8564 (tttt) cc_final: 0.8203 (tptp) REVERT: D 109 LYS cc_start: 0.8572 (tttt) cc_final: 0.8211 (tptp) REVERT: D 193 GLN cc_start: 0.8296 (pt0) cc_final: 0.8003 (pm20) REVERT: D 395 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8371 (m-30) REVERT: E 109 LYS cc_start: 0.8565 (tttt) cc_final: 0.8208 (tptp) REVERT: E 193 GLN cc_start: 0.8260 (pt0) cc_final: 0.7938 (pm20) outliers start: 26 outliers final: 13 residues processed: 145 average time/residue: 2.4802 time to fit residues: 399.7024 Evaluate side-chains 144 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 134 LEU 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 395 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 117 THR 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: 3.9990 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14140 Z= 0.189 Angle : 0.441 6.194 19245 Z= 0.228 Chirality : 0.039 0.121 2160 Planarity : 0.004 0.035 2395 Dihedral : 3.846 18.958 2030 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.74 % Allowed : 8.12 % Favored : 90.13 % 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: 2.04 (0.21), residues: 1670 helix: 3.21 (0.21), residues: 580 sheet: 0.45 (0.25), residues: 455 loop : 0.35 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 73 HIS 0.003 0.001 HIS C 195 PHE 0.009 0.001 PHE C 307 TYR 0.007 0.001 TYR E 413 ARG 0.001 0.000 ARG C 277 *********************** 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 155 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 2.491 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: A 109 LYS cc_start: 0.8542 (tttt) cc_final: 0.8190 (tptp) REVERT: A 134 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8936 (pt) REVERT: A 151 MET cc_start: 0.9035 (mpt) cc_final: 0.8827 (mpt) REVERT: A 193 GLN cc_start: 0.8271 (pt0) cc_final: 0.7978 (pm20) REVERT: B 109 LYS cc_start: 0.8520 (tttt) cc_final: 0.8159 (tptp) REVERT: B 193 GLN cc_start: 0.8228 (pt0) cc_final: 0.7975 (pm20) REVERT: C 109 LYS cc_start: 0.8571 (tttt) cc_final: 0.8203 (tptp) REVERT: D 109 LYS cc_start: 0.8567 (tttt) cc_final: 0.8226 (tptp) REVERT: D 193 GLN cc_start: 0.8296 (pt0) cc_final: 0.8000 (pm20) REVERT: D 395 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8347 (m-30) REVERT: E 109 LYS cc_start: 0.8555 (tttt) cc_final: 0.8185 (tptp) REVERT: E 193 GLN cc_start: 0.8259 (pt0) cc_final: 0.7936 (pm20) outliers start: 26 outliers final: 13 residues processed: 138 average time/residue: 2.4218 time to fit residues: 373.6053 Evaluate side-chains 136 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14140 Z= 0.224 Angle : 0.450 5.892 19245 Z= 0.233 Chirality : 0.039 0.121 2160 Planarity : 0.004 0.035 2395 Dihedral : 3.976 19.216 2030 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.61 % Allowed : 8.93 % Favored : 89.46 % 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: 2.00 (0.21), residues: 1670 helix: 3.20 (0.21), residues: 580 sheet: 0.33 (0.24), residues: 465 loop : 0.39 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 73 HIS 0.003 0.001 HIS C 195 PHE 0.010 0.001 PHE A 104 TYR 0.008 0.001 TYR E 413 ARG 0.001 0.000 ARG C 277 *********************** 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 153 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 2.116 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: A 134 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8992 (pt) REVERT: A 147 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7977 (tp30) REVERT: A 193 GLN cc_start: 0.8274 (pt0) cc_final: 0.7972 (pm20) REVERT: B 109 LYS cc_start: 0.8506 (tttt) cc_final: 0.8140 (tptp) REVERT: B 193 GLN cc_start: 0.8248 (pt0) cc_final: 0.7967 (pm20) REVERT: C 109 LYS cc_start: 0.8561 (tttt) cc_final: 0.8181 (tptp) REVERT: D 109 LYS cc_start: 0.8537 (tttt) cc_final: 0.8191 (tptp) REVERT: D 193 GLN cc_start: 0.8310 (pt0) cc_final: 0.7998 (pm20) REVERT: D 395 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8369 (m-30) REVERT: E 193 GLN cc_start: 0.8279 (pt0) cc_final: 0.7944 (pm20) outliers start: 24 outliers final: 13 residues processed: 136 average time/residue: 2.3202 time to fit residues: 353.1424 Evaluate side-chains 143 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 117 THR 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: 0.8980 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14140 Z= 0.224 Angle : 0.451 5.909 19245 Z= 0.233 Chirality : 0.039 0.120 2160 Planarity : 0.004 0.035 2395 Dihedral : 3.992 19.538 2030 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.74 % Allowed : 8.79 % Favored : 89.46 % 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: 2.00 (0.21), residues: 1670 helix: 3.19 (0.21), residues: 580 sheet: 0.34 (0.24), residues: 465 loop : 0.39 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 73 HIS 0.003 0.001 HIS C 195 PHE 0.010 0.001 PHE A 104 TYR 0.008 0.001 TYR E 413 ARG 0.001 0.000 ARG E 123 *********************** 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 156 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 2.349 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: A 134 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8994 (pt) REVERT: A 147 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: A 193 GLN cc_start: 0.8285 (pt0) cc_final: 0.7986 (pm20) REVERT: B 109 LYS cc_start: 0.8508 (tttt) cc_final: 0.8150 (tptp) REVERT: B 193 GLN cc_start: 0.8249 (pt0) cc_final: 0.7992 (pm20) REVERT: D 193 GLN cc_start: 0.8322 (pt0) cc_final: 0.8002 (pm20) REVERT: D 395 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: E 193 GLN cc_start: 0.8296 (pt0) cc_final: 0.7970 (pm20) outliers start: 26 outliers final: 14 residues processed: 138 average time/residue: 2.2881 time to fit residues: 353.4888 Evaluate side-chains 140 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 280 LEU 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: 1.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14140 Z= 0.263 Angle : 0.466 6.088 19245 Z= 0.242 Chirality : 0.040 0.122 2160 Planarity : 0.004 0.035 2395 Dihedral : 4.164 22.209 2030 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.01 % Allowed : 8.66 % Favored : 89.33 % 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: 1.93 (0.21), residues: 1670 helix: 3.09 (0.21), residues: 585 sheet: 0.30 (0.24), residues: 465 loop : 0.38 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 73 HIS 0.003 0.001 HIS C 195 PHE 0.011 0.001 PHE A 104 TYR 0.008 0.001 TYR A 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 155 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 2.266 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: A 134 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8990 (pt) REVERT: A 147 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7970 (tp30) REVERT: A 193 GLN cc_start: 0.8299 (pt0) cc_final: 0.7986 (pm20) REVERT: B 193 GLN cc_start: 0.8275 (pt0) cc_final: 0.8006 (pm20) REVERT: D 193 GLN cc_start: 0.8350 (pt0) cc_final: 0.8014 (pm20) REVERT: D 395 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: E 193 GLN cc_start: 0.8327 (pt0) cc_final: 0.7993 (pm20) outliers start: 30 outliers final: 19 residues processed: 138 average time/residue: 2.1589 time to fit residues: 338.3377 Evaluate side-chains 144 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E 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: 2.9990 chunk 139 optimal weight: 1.9990 chunk 148 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14140 Z= 0.172 Angle : 0.435 5.646 19245 Z= 0.224 Chirality : 0.039 0.120 2160 Planarity : 0.003 0.036 2395 Dihedral : 3.859 19.214 2030 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.41 % Allowed : 9.46 % Favored : 89.13 % 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: 2.05 (0.21), residues: 1670 helix: 3.16 (0.21), residues: 585 sheet: 0.43 (0.25), residues: 455 loop : 0.41 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 73 HIS 0.002 0.001 HIS C 195 PHE 0.008 0.001 PHE C 307 TYR 0.007 0.001 TYR A 413 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 144 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 2.408 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: A 134 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9013 (pt) REVERT: A 193 GLN cc_start: 0.8281 (pt0) cc_final: 0.7975 (pm20) REVERT: B 193 GLN cc_start: 0.8236 (pt0) cc_final: 0.7971 (pm20) REVERT: B 251 ASN cc_start: 0.8101 (p0) cc_final: 0.7627 (p0) REVERT: C 134 LEU cc_start: 0.9136 (tp) cc_final: 0.8918 (pt) REVERT: D 134 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9022 (pp) REVERT: D 193 GLN cc_start: 0.8320 (pt0) cc_final: 0.8003 (pm20) REVERT: D 395 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8342 (m-30) REVERT: E 193 GLN cc_start: 0.8300 (pt0) cc_final: 0.7968 (pm20) outliers start: 21 outliers final: 14 residues processed: 132 average time/residue: 2.1868 time to fit residues: 325.7545 Evaluate side-chains 139 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 395 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14140 Z= 0.145 Angle : 0.425 5.302 19245 Z= 0.217 Chirality : 0.039 0.121 2160 Planarity : 0.003 0.036 2395 Dihedral : 3.659 18.705 2030 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.21 % Allowed : 9.60 % Favored : 89.19 % 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: 2.27 (0.21), residues: 1670 helix: 3.32 (0.20), residues: 615 sheet: 0.49 (0.25), residues: 455 loop : 0.47 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 414 HIS 0.003 0.001 HIS C 195 PHE 0.008 0.001 PHE A 261 TYR 0.009 0.001 TYR E 297 ARG 0.002 0.000 ARG A 120 ********************** 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 136 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.794 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: A 193 GLN cc_start: 0.8294 (pt0) cc_final: 0.7979 (pm20) REVERT: B 193 GLN cc_start: 0.8251 (pt0) cc_final: 0.7976 (pm20) REVERT: B 251 ASN cc_start: 0.8048 (p0) cc_final: 0.7581 (p0) REVERT: D 193 GLN cc_start: 0.8315 (pt0) cc_final: 0.8018 (pm20) REVERT: D 395 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: E 193 GLN cc_start: 0.8281 (pt0) cc_final: 0.7947 (pm20) outliers start: 18 outliers final: 13 residues processed: 131 average time/residue: 2.1921 time to fit residues: 322.5073 Evaluate side-chains 126 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.080892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.067191 restraints weight = 74298.173| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.34 r_work: 0.2801 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14140 Z= 0.168 Angle : 0.430 5.396 19245 Z= 0.221 Chirality : 0.039 0.120 2160 Planarity : 0.003 0.036 2395 Dihedral : 3.718 18.767 2030 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.21 % Allowed : 9.73 % Favored : 89.06 % 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: 2.27 (0.21), residues: 1670 helix: 3.33 (0.20), residues: 615 sheet: 0.49 (0.25), residues: 455 loop : 0.44 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 414 HIS 0.003 0.001 HIS C 195 PHE 0.008 0.001 PHE C 307 TYR 0.007 0.001 TYR E 413 ARG 0.001 0.000 ARG B 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8704.21 seconds wall clock time: 153 minutes 23.38 seconds (9203.38 seconds total)