Starting phenix.real_space_refine on Sat Jul 4 13:23:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ejf_48102/07_2026/9ejf_48102.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ejf_48102/07_2026/9ejf_48102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ejf_48102/07_2026/9ejf_48102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ejf_48102/07_2026/9ejf_48102.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ejf_48102/07_2026/9ejf_48102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ejf_48102/07_2026/9ejf_48102.map" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 Ca 8 9.91 5 S 108 5.16 5 C 12236 2.51 5 N 3260 2.21 5 O 4742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20354 Number of models: 1 Model: "" Number of chains: 32 Chain: "D" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2951 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2951 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "F" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2951 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 980 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "I" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 980 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "J" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 980 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "K" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2951 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "L" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 980 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 154 Classifications: {'water': 154} Link IDs: {None: 153} Chain: "F" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 146 Classifications: {'water': 146} Link IDs: {None: 145} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "J" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "K" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "N" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Time building chain proxies: 3.69, per 1000 atoms: 0.18 Number of scatterers: 20354 At special positions: 0 Unit cell: (140.715, 137.175, 85.845, 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) Ca 8 19.99 S 108 16.00 O 4742 8.00 N 3260 7.00 C 12236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.03 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.03 Simple disulfide: pdb=" SG CYS E 279 " - pdb=" SG CYS E 292 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 290 " distance=2.03 Simple disulfide: pdb=" SG CYS F 124 " - pdb=" SG CYS F 129 " distance=2.04 Simple disulfide: pdb=" SG CYS F 279 " - pdb=" SG CYS F 292 " distance=2.03 Simple disulfide: pdb=" SG CYS F 281 " - pdb=" SG CYS F 290 " distance=2.03 Simple disulfide: pdb=" SG CYS K 124 " - pdb=" SG CYS K 129 " distance=2.03 Simple disulfide: pdb=" SG CYS K 279 " - pdb=" SG CYS K 292 " distance=2.03 Simple disulfide: pdb=" SG CYS K 281 " - pdb=" SG CYS K 290 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 1 " - " ASN D 146 " " NAG B 1 " - " ASN E 146 " " NAG C 1 " - " ASN F 146 " " NAG D 501 " - " ASN D 88 " " NAG D 502 " - " ASN D 235 " " NAG E 501 " - " ASN E 88 " " NAG E 502 " - " ASN E 235 " " NAG F 501 " - " ASN F 88 " " NAG F 502 " - " ASN F 235 " " NAG G 1 " - " ASN K 146 " " NAG K 501 " - " ASN K 88 " " NAG K 502 " - " ASN K 235 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 775.3 milliseconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4472 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 49 sheets defined 4.8% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 409 through 414 Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 409 through 414 Processing helix chain 'F' and resid 104 through 109 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 409 through 414 Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 104 through 109 Processing helix chain 'K' and resid 142 through 146 Processing helix chain 'K' and resid 409 through 414 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.806A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.764A pdb=" N VAL M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.728A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.735A pdb=" N LYS O 64 " --> pdb=" O PRO O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.776A pdb=" N VAL P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 96 through 103 removed outlier: 6.586A pdb=" N SER D 444 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.670A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR D 157 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER D 160 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N PHE D 174 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 180 through 185 removed outlier: 3.507A pdb=" N SER D 180 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP D 214 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR D 208 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 232 through 234 removed outlier: 6.517A pdb=" N GLU D 259 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 277 through 284 removed outlier: 4.855A pdb=" N CYS D 279 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL D 291 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N CYS D 281 " --> pdb=" O THR D 289 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR D 289 " --> pdb=" O CYS D 281 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU D 287 " --> pdb=" O PRO D 283 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 353 removed outlier: 7.371A pdb=" N GLU D 398 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLU D 372 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 11.097A pdb=" N ILE D 396 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 11.493A pdb=" N ILE D 374 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 13.656A pdb=" N VAL D 394 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 15.051A pdb=" N ASP D 376 " --> pdb=" O ASP D 392 " (cutoff:3.500A) removed outlier: 16.037A pdb=" N ASP D 392 " --> pdb=" O ASP D 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 96 through 103 removed outlier: 6.589A pdb=" N SER E 444 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS E 102 " --> pdb=" O SER E 442 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N SER E 442 " --> pdb=" O LYS E 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 115 through 124 removed outlier: 4.704A pdb=" N PHE E 115 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ALA E 138 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN E 136 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER E 160 " --> pdb=" O PHE E 174 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N PHE E 174 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 180 through 185 removed outlier: 3.522A pdb=" N SER E 180 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP E 214 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR E 208 " --> pdb=" O ILE E 212 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE E 212 " --> pdb=" O TYR E 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 232 through 234 removed outlier: 3.565A pdb=" N LYS E 265 " --> pdb=" O ARG E 257 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU E 259 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILE E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 277 through 284 removed outlier: 4.791A pdb=" N CYS E 279 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL E 291 " --> pdb=" O CYS E 279 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS E 281 " --> pdb=" O THR E 289 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR E 289 " --> pdb=" O CYS E 281 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU E 287 " --> pdb=" O PRO E 283 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 350 through 353 removed outlier: 7.302A pdb=" N GLU E 398 " --> pdb=" O GLY E 370 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N GLU E 372 " --> pdb=" O ILE E 396 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N ILE E 396 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N ILE E 374 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 13.824A pdb=" N VAL E 394 " --> pdb=" O ILE E 374 " (cutoff:3.500A) removed outlier: 14.824A pdb=" N ASP E 376 " --> pdb=" O ASP E 392 " (cutoff:3.500A) removed outlier: 15.967A pdb=" N ASP E 392 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 96 through 102 removed outlier: 6.584A pdb=" N SER F 444 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS F 102 " --> pdb=" O SER F 442 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N SER F 442 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 115 through 124 removed outlier: 4.650A pdb=" N PHE F 115 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA F 138 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE F 117 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN F 136 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLU F 119 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU F 134 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER F 176 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER F 160 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N PHE F 174 " --> pdb=" O SER F 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 180 through 185 removed outlier: 3.555A pdb=" N SER F 180 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA F 204 " --> pdb=" O THR F 215 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR F 215 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU F 206 " --> pdb=" O THR F 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 225 through 226 removed outlier: 3.566A pdb=" N ALA F 232 " --> pdb=" O PHE F 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 225 through 226 removed outlier: 3.542A pdb=" N LYS F 265 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU F 259 " --> pdb=" O ILE F 263 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE F 263 " --> pdb=" O GLU F 259 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 277 through 284 removed outlier: 4.986A pdb=" N CYS F 279 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL F 291 " --> pdb=" O CYS F 279 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N CYS F 281 " --> pdb=" O THR F 289 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR F 289 " --> pdb=" O CYS F 281 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU F 287 " --> pdb=" O PRO F 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 350 through 353 removed outlier: 6.708A pdb=" N ASN F 369 " --> pdb=" O GLY F 395 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLY F 395 " --> pdb=" O ASN F 369 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE F 371 " --> pdb=" O ILE F 393 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.240A pdb=" N TRP H 35A" --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.872A pdb=" N CYS H 92 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL H 102 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG H 94 " --> pdb=" O LEU H 100I" (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU H 100I" --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY H 96 " --> pdb=" O LEU H 100G" (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR H 100E" --> pdb=" O SER H 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.072A pdb=" N TRP I 35A" --> pdb=" O ASN I 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN I 50 " --> pdb=" O TRP I 35A" (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.910A pdb=" N CYS I 92 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL I 102 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG I 94 " --> pdb=" O LEU I 100I" (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU I 100I" --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY I 96 " --> pdb=" O LEU I 100G" (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR I 100E" --> pdb=" O SER I 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.763A pdb=" N SER J 70 " --> pdb=" O TYR J 79 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.290A pdb=" N TRP J 35A" --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.856A pdb=" N CYS J 92 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL J 102 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG J 94 " --> pdb=" O LEU J 100I" (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU J 100I" --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY J 96 " --> pdb=" O LEU J 100G" (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR J 100E" --> pdb=" O SER J 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 96 through 102 removed outlier: 6.608A pdb=" N SER K 444 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS K 102 " --> pdb=" O SER K 442 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N SER K 442 " --> pdb=" O LYS K 102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 115 through 124 removed outlier: 4.697A pdb=" N PHE K 115 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA K 138 " --> pdb=" O PHE K 115 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE K 117 " --> pdb=" O GLN K 136 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN K 136 " --> pdb=" O ILE K 117 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU K 119 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU K 134 " --> pdb=" O GLU K 119 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR K 157 " --> pdb=" O THR K 135 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N SER K 160 " --> pdb=" O PHE K 174 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE K 174 " --> pdb=" O SER K 160 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 180 through 185 removed outlier: 3.553A pdb=" N SER K 180 " --> pdb=" O ILE K 195 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP K 214 " --> pdb=" O LEU K 206 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR K 208 " --> pdb=" O ILE K 212 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE K 212 " --> pdb=" O TYR K 208 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 232 through 234 removed outlier: 6.542A pdb=" N GLU K 259 " --> pdb=" O ILE K 263 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE K 263 " --> pdb=" O GLU K 259 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 277 through 284 removed outlier: 5.021A pdb=" N CYS K 279 " --> pdb=" O VAL K 291 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL K 291 " --> pdb=" O CYS K 279 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N CYS K 281 " --> pdb=" O THR K 289 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR K 289 " --> pdb=" O CYS K 281 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU K 287 " --> pdb=" O PRO K 283 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 350 through 353 removed outlier: 6.665A pdb=" N ASN K 369 " --> pdb=" O GLY K 395 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLY K 395 " --> pdb=" O ASN K 369 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE K 371 " --> pdb=" O ILE K 393 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.598A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.598A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.514A pdb=" N GLY M 84 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU M 33 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.514A pdb=" N GLY M 84 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.528A pdb=" N GLY N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.528A pdb=" N GLY N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'O' and resid 11 through 12 removed outlier: 8.248A pdb=" N TYR O 34 " --> pdb=" O PHE O 52 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE O 52 " --> pdb=" O TYR O 34 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TRP O 35A" --> pdb=" O ASN O 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN O 50 " --> pdb=" O TRP O 35A" (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.705A pdb=" N CYS O 92 " --> pdb=" O VAL O 102 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL O 102 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG O 94 " --> pdb=" O LEU O 100I" (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU O 100I" --> pdb=" O ARG O 94 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY O 96 " --> pdb=" O LEU O 100G" (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR O 100E" --> pdb=" O SER O 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.541A pdb=" N GLY P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU P 46 " --> pdb=" O LEU P 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.541A pdb=" N GLY P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) 701 hydrogen bonds defined for protein. 1773 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: 3.69 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5882 1.34 - 1.46: 5394 1.46 - 1.59: 8526 1.59 - 1.72: 2 1.72 - 1.84: 136 Bond restraints: 19940 Sorted by residual: bond pdb=" CA TYR K 208 " pdb=" CB TYR K 208 " ideal model delta sigma weight residual 1.532 1.663 -0.131 1.58e-02 4.01e+03 6.89e+01 bond pdb=" CG TYR E 353 " pdb=" CD2 TYR E 353 " ideal model delta sigma weight residual 1.389 1.552 -0.163 2.10e-02 2.27e+03 6.00e+01 bond pdb=" CG TYR E 353 " pdb=" CD1 TYR E 353 " ideal model delta sigma weight residual 1.389 1.247 0.142 2.10e-02 2.27e+03 4.56e+01 bond pdb=" C VAL H 12 " pdb=" N LYS H 13 " ideal model delta sigma weight residual 1.327 1.488 -0.161 2.86e-02 1.22e+03 3.17e+01 bond pdb=" CA TYR E 353 " pdb=" CB TYR E 353 " ideal model delta sigma weight residual 1.524 1.446 0.078 1.62e-02 3.81e+03 2.32e+01 ... (remaining 19935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 26570 3.26 - 6.52: 534 6.52 - 9.78: 33 9.78 - 13.03: 6 13.03 - 16.29: 5 Bond angle restraints: 27148 Sorted by residual: angle pdb=" CB TYR E 353 " pdb=" CG TYR E 353 " pdb=" CD2 TYR E 353 " ideal model delta sigma weight residual 120.80 104.51 16.29 1.50e+00 4.44e-01 1.18e+02 angle pdb=" CB TYR E 353 " pdb=" CG TYR E 353 " pdb=" CD1 TYR E 353 " ideal model delta sigma weight residual 120.80 134.12 -13.32 1.50e+00 4.44e-01 7.89e+01 angle pdb=" CA TYR K 208 " pdb=" CB TYR K 208 " pdb=" CG TYR K 208 " ideal model delta sigma weight residual 113.90 98.92 14.98 1.80e+00 3.09e-01 6.93e+01 angle pdb=" CB TYR O 34 " pdb=" CG TYR O 34 " pdb=" CD1 TYR O 34 " ideal model delta sigma weight residual 120.80 131.06 -10.26 1.50e+00 4.44e-01 4.68e+01 angle pdb=" CB TYR O 34 " pdb=" CG TYR O 34 " pdb=" CD2 TYR O 34 " ideal model delta sigma weight residual 120.80 111.48 9.32 1.50e+00 4.44e-01 3.86e+01 ... (remaining 27143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 11020 19.02 - 38.05: 681 38.05 - 57.07: 117 57.07 - 76.09: 59 76.09 - 95.12: 35 Dihedral angle restraints: 11912 sinusoidal: 4868 harmonic: 7044 Sorted by residual: dihedral pdb=" CA TRP I 35A" pdb=" C TRP I 35A" pdb=" N THR I 35B" pdb=" CA THR I 35B" ideal model delta harmonic sigma weight residual -180.00 -150.79 -29.21 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA GLY F 342 " pdb=" C GLY F 342 " pdb=" N ALA F 343 " pdb=" CA ALA F 343 " ideal model delta harmonic sigma weight residual 180.00 -154.34 -25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA PHE E 115 " pdb=" C PHE E 115 " pdb=" N VAL E 116 " pdb=" CA VAL E 116 " ideal model delta harmonic sigma weight residual 180.00 155.32 24.68 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 11909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2667 0.105 - 0.209: 285 0.209 - 0.314: 27 0.314 - 0.419: 2 0.419 - 0.523: 3 Chirality restraints: 2984 Sorted by residual: chirality pdb=" CG LEU M 47 " pdb=" CB LEU M 47 " pdb=" CD1 LEU M 47 " pdb=" CD2 LEU M 47 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" CB ILE I 48 " pdb=" CA ILE I 48 " pdb=" CG1 ILE I 48 " pdb=" CG2 ILE I 48 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" CB ILE E 365 " pdb=" CA ILE E 365 " pdb=" CG1 ILE E 365 " pdb=" CG2 ILE E 365 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.23e+00 ... (remaining 2981 not shown) Planarity restraints: 3484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 208 " 0.140 2.00e-02 2.50e+03 9.87e-02 1.95e+02 pdb=" CG TYR K 208 " -0.227 2.00e-02 2.50e+03 pdb=" CD1 TYR K 208 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR K 208 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR K 208 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR K 208 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR K 208 " 0.081 2.00e-02 2.50e+03 pdb=" OH TYR K 208 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 79 " -0.096 2.00e-02 2.50e+03 6.65e-02 8.84e+01 pdb=" CG TYR J 79 " 0.143 2.00e-02 2.50e+03 pdb=" CD1 TYR J 79 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR J 79 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 79 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR J 79 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR J 79 " -0.074 2.00e-02 2.50e+03 pdb=" OH TYR J 79 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 353 " -0.107 2.00e-02 2.50e+03 6.57e-02 8.63e+01 pdb=" CG TYR E 353 " 0.145 2.00e-02 2.50e+03 pdb=" CD1 TYR E 353 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR E 353 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR E 353 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 353 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR E 353 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 353 " -0.039 2.00e-02 2.50e+03 ... (remaining 3481 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 369 2.67 - 3.23: 18584 3.23 - 3.78: 32970 3.78 - 4.34: 51991 4.34 - 4.90: 79514 Nonbonded interactions: 183428 Sorted by model distance: nonbonded pdb=" OD1 ASN F 378 " pdb="CA CA F 504 " model vdw 2.108 3.250 nonbonded pdb=" OD1 ASN D 378 " pdb="CA CA D 504 " model vdw 2.159 3.250 nonbonded pdb=" OD1 ASN K 378 " pdb="CA CA K 504 " model vdw 2.180 3.250 nonbonded pdb=" O SER D 165 " pdb=" O HOH D 601 " model vdw 2.190 3.040 nonbonded pdb=" OD1 ASP F 376 " pdb="CA CA F 504 " model vdw 2.232 3.250 ... (remaining 183423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' } 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: 8.970 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.890 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5674 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.163 19972 Z= 0.355 Angle : 1.152 16.293 27232 Z= 0.628 Chirality : 0.068 0.523 2984 Planarity : 0.014 0.211 3472 Dihedral : 14.783 95.116 7404 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.96 % Favored : 94.59 % Rotamer: Outliers : 2.94 % Allowed : 5.84 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.15), residues: 2460 helix: -3.45 (0.43), residues: 24 sheet: -0.57 (0.16), residues: 968 loop : -1.60 (0.14), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.073 0.003 ARG F 257 TYR 0.227 0.007 TYR K 208 PHE 0.053 0.004 PHE J 52 TRP 0.088 0.005 TRP N 96 HIS 0.036 0.004 HIS M 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00770 / 0.35 (19940) covalent geometry : angle 1.14283 / 0.63 (27148) SS BOND : bond 0.00225 / 0.10 ( 12) SS BOND : angle 1.09493 / 0.62 ( 24) hydrogen bonds : bond 0.17204 / 11.55 ( 655) hydrogen bonds : angle 8.98404 / 6.32 ( 1773) link_BETA1-4 : bond 0.02445 / 1.19 ( 8) link_BETA1-4 : angle 3.28608 / 2.02 ( 24) link_NAG-ASN : bond 0.01017 / 0.64 ( 12) link_NAG-ASN : angle 3.19657 / 2.15 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 348 time to evaluate : 0.780 Fit side-chains REVERT: D 89 SER cc_start: 0.7405 (m) cc_final: 0.7069 (p) REVERT: D 93 PRO cc_start: 0.6491 (Cg_exo) cc_final: 0.6249 (Cg_endo) REVERT: D 142 ASP cc_start: 0.5720 (t70) cc_final: 0.5414 (t70) REVERT: D 220 ARG cc_start: 0.5431 (mmt90) cc_final: 0.4485 (mmt90) REVERT: D 230 GLU cc_start: 0.5824 (tt0) cc_final: 0.5559 (pt0) REVERT: D 257 ARG cc_start: 0.6974 (ttt180) cc_final: 0.6689 (ttt180) REVERT: D 260 LYS cc_start: 0.6027 (mttm) cc_final: 0.5561 (mttt) REVERT: D 287 GLU cc_start: 0.6366 (mt-10) cc_final: 0.5991 (mt-10) REVERT: D 305 SER cc_start: 0.6288 (t) cc_final: 0.5836 (p) REVERT: D 355 ASN cc_start: 0.6007 (m-40) cc_final: 0.5804 (t0) REVERT: D 449 ASN cc_start: 0.7209 (t0) cc_final: 0.6860 (m110) REVERT: D 462 GLU cc_start: 0.5535 (mt-10) cc_final: 0.5044 (mp0) REVERT: E 89 SER cc_start: 0.7473 (m) cc_final: 0.7038 (p) REVERT: E 142 ASP cc_start: 0.5299 (t70) cc_final: 0.5098 (t70) REVERT: E 220 ARG cc_start: 0.5263 (mmt90) cc_final: 0.4398 (mmt90) REVERT: E 257 ARG cc_start: 0.7010 (ttt180) cc_final: 0.6749 (ttt180) REVERT: E 260 LYS cc_start: 0.6194 (mttm) cc_final: 0.5759 (mttt) REVERT: E 287 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6215 (mt-10) REVERT: E 305 SER cc_start: 0.6264 (t) cc_final: 0.5219 (p) REVERT: E 313 GLN cc_start: 0.6452 (mt0) cc_final: 0.4748 (mp10) REVERT: E 355 ASN cc_start: 0.6167 (m-40) cc_final: 0.5958 (t0) REVERT: E 450 SER cc_start: 0.6954 (OUTLIER) cc_final: 0.6474 (p) REVERT: E 462 GLU cc_start: 0.5634 (mt-10) cc_final: 0.5058 (mp0) REVERT: F 89 SER cc_start: 0.7432 (m) cc_final: 0.7116 (p) REVERT: F 117 ILE cc_start: 0.5907 (OUTLIER) cc_final: 0.5692 (pp) REVERT: F 220 ARG cc_start: 0.5408 (mmt90) cc_final: 0.4513 (mmt90) REVERT: F 230 GLU cc_start: 0.5647 (tt0) cc_final: 0.5201 (pt0) REVERT: F 260 LYS cc_start: 0.6137 (mttm) cc_final: 0.5614 (mttt) REVERT: F 287 GLU cc_start: 0.6485 (mt-10) cc_final: 0.5951 (mt-10) REVERT: F 305 SER cc_start: 0.6755 (t) cc_final: 0.6492 (p) REVERT: F 449 ASN cc_start: 0.7279 (t0) cc_final: 0.6938 (m110) REVERT: F 450 SER cc_start: 0.7186 (m) cc_final: 0.6888 (p) REVERT: F 462 GLU cc_start: 0.5363 (mt-10) cc_final: 0.4947 (mp0) REVERT: H 5 GLN cc_start: 0.6094 (tt0) cc_final: 0.5303 (mm-40) REVERT: H 27 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6090 (pt0) REVERT: H 58 ASP cc_start: 0.7575 (t0) cc_final: 0.7229 (t70) REVERT: H 74 SER cc_start: 0.7910 (p) cc_final: 0.7516 (p) REVERT: H 76 ASN cc_start: 0.6172 (m-40) cc_final: 0.5969 (t0) REVERT: I 4 LEU cc_start: 0.6799 (mt) cc_final: 0.6567 (mt) REVERT: I 5 GLN cc_start: 0.6051 (tt0) cc_final: 0.5238 (mm-40) REVERT: I 27 GLU cc_start: 0.6571 (mt-10) cc_final: 0.5755 (pt0) REVERT: I 58 ASP cc_start: 0.7581 (t0) cc_final: 0.7246 (t70) REVERT: I 74 SER cc_start: 0.7786 (p) cc_final: 0.7351 (p) REVERT: J 4 LEU cc_start: 0.6726 (mt) cc_final: 0.6509 (mt) REVERT: J 5 GLN cc_start: 0.6073 (tt0) cc_final: 0.5116 (mm-40) REVERT: J 19 SER cc_start: 0.7356 (m) cc_final: 0.7019 (p) REVERT: J 27 GLU cc_start: 0.6742 (mt-10) cc_final: 0.5853 (pt0) REVERT: J 58 ASP cc_start: 0.7773 (t0) cc_final: 0.7471 (t0) REVERT: J 74 SER cc_start: 0.7844 (p) cc_final: 0.7049 (t) REVERT: K 220 ARG cc_start: 0.5387 (mmt90) cc_final: 0.4550 (mmt90) REVERT: K 257 ARG cc_start: 0.6986 (ttt180) cc_final: 0.6773 (ttt180) REVERT: K 260 LYS cc_start: 0.6106 (mttm) cc_final: 0.5658 (mttt) REVERT: K 287 GLU cc_start: 0.6285 (mt-10) cc_final: 0.5216 (tt0) REVERT: K 450 SER cc_start: 0.7001 (m) cc_final: 0.6798 (p) REVERT: L 50 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.5245 (t80) REVERT: M 50 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.5145 (t80) REVERT: N 50 PHE cc_start: 0.6785 (OUTLIER) cc_final: 0.5055 (t80) REVERT: O 5 GLN cc_start: 0.6008 (tt0) cc_final: 0.5188 (mm-40) REVERT: O 58 ASP cc_start: 0.7579 (t0) cc_final: 0.7216 (t70) REVERT: O 74 SER cc_start: 0.7791 (p) cc_final: 0.7089 (t) REVERT: P 50 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.5176 (t80) outliers start: 63 outliers final: 27 residues processed: 405 average time/residue: 0.4691 time to fit residues: 220.9942 Evaluate side-chains 278 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 297 HIS Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 231 CYS Chi-restraints excluded: chain E residue 297 HIS Chi-restraints excluded: chain E residue 410 PRO Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 297 HIS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 231 CYS Chi-restraints excluded: chain L residue 40 PRO Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.0770 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 144 HIS D 189 ASN D 200 ASN E 144 HIS E 189 ASN E 297 HIS F 144 HIS F 189 ASN F 200 ASN H 5 GLN I 77 GLN K 144 HIS K 189 ASN K 297 HIS L 6 GLN M 6 GLN N 6 GLN P 6 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118832 restraints weight = 18269.217| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.39 r_work: 0.3173 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19972 Z= 0.150 Angle : 0.678 12.118 27232 Z= 0.353 Chirality : 0.049 0.169 2984 Planarity : 0.005 0.056 3472 Dihedral : 8.556 59.911 3145 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.48 % Favored : 97.36 % Rotamer: Outliers : 2.99 % Allowed : 9.02 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2460 helix: -1.40 (0.77), residues: 24 sheet: -0.00 (0.16), residues: 1044 loop : -0.77 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 173 TYR 0.012 0.002 TYR E 253 PHE 0.017 0.002 PHE K 406 TRP 0.020 0.002 TRP O 47 HIS 0.005 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (19940) covalent geometry : angle 0.66911 / 0.35 (27148) SS BOND : bond 0.00281 / 0.16 ( 12) SS BOND : angle 0.65504 / 0.44 ( 24) hydrogen bonds : bond 0.04218 / 2.90 ( 655) hydrogen bonds : angle 6.45597 / 4.52 ( 1773) link_BETA1-4 : bond 0.00498 / 0.23 ( 8) link_BETA1-4 : angle 2.66988 / 1.78 ( 24) link_NAG-ASN : bond 0.00781 / 0.46 ( 12) link_NAG-ASN : angle 2.34520 / 1.51 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 295 time to evaluate : 0.572 Fit side-chains REVERT: D 220 ARG cc_start: 0.8065 (mmt90) cc_final: 0.7627 (mmt90) REVERT: D 287 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7987 (mt-10) REVERT: D 293 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7596 (ttp-170) REVERT: E 220 ARG cc_start: 0.8081 (mmt90) cc_final: 0.7720 (mmt90) REVERT: E 287 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8099 (mt-10) REVERT: E 434 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7225 (m-40) REVERT: F 220 ARG cc_start: 0.8077 (mmt90) cc_final: 0.7565 (mmt90) REVERT: F 287 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8014 (mt-10) REVERT: F 293 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.6770 (ttm170) REVERT: F 355 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8078 (m-40) REVERT: H 5 GLN cc_start: 0.7083 (tt0) cc_final: 0.6577 (mm-40) REVERT: H 74 SER cc_start: 0.7806 (p) cc_final: 0.7362 (t) REVERT: I 5 GLN cc_start: 0.7096 (tt0) cc_final: 0.6503 (mm-40) REVERT: I 27 GLU cc_start: 0.7659 (mt-10) cc_final: 0.6977 (pt0) REVERT: I 74 SER cc_start: 0.7877 (p) cc_final: 0.7394 (t) REVERT: J 74 SER cc_start: 0.7894 (p) cc_final: 0.7421 (t) REVERT: K 220 ARG cc_start: 0.8122 (mmt90) cc_final: 0.7615 (mmt90) REVERT: K 287 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8119 (mt-10) REVERT: M 10 SER cc_start: 0.7436 (t) cc_final: 0.7099 (m) REVERT: N 10 SER cc_start: 0.7445 (t) cc_final: 0.7102 (m) REVERT: O 5 GLN cc_start: 0.7137 (tt0) cc_final: 0.6592 (mm-40) REVERT: O 27 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6932 (pt0) REVERT: O 74 SER cc_start: 0.7899 (p) cc_final: 0.7493 (t) outliers start: 64 outliers final: 25 residues processed: 344 average time/residue: 0.5202 time to fit residues: 204.3779 Evaluate side-chains 269 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 434 ASN Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 293 ARG Chi-restraints excluded: chain F residue 297 HIS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 118 ARG Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain K residue 297 HIS Chi-restraints excluded: chain K residue 442 SER Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain P residue 50 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 213 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 144 HIS E 144 HIS F 144 HIS F 297 HIS H 77 GLN I 77 GLN K 144 HIS K 369 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109118 restraints weight = 18128.878| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.35 r_work: 0.3015 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19972 Z= 0.209 Angle : 0.773 8.048 27232 Z= 0.405 Chirality : 0.054 0.272 2984 Planarity : 0.006 0.049 3472 Dihedral : 7.510 56.860 3118 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 2.90 % Allowed : 11.12 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2460 helix: -1.25 (0.94), residues: 24 sheet: 0.19 (0.16), residues: 1032 loop : -0.62 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 130 TYR 0.023 0.002 TYR E 353 PHE 0.028 0.003 PHE H 78 TRP 0.014 0.002 TRP I 47 HIS 0.006 0.002 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (19940) covalent geometry : angle 0.76363 / 0.40 (27148) SS BOND : bond 0.00330 / 0.18 ( 12) SS BOND : angle 1.09795 / 0.66 ( 24) hydrogen bonds : bond 0.05286 / 3.61 ( 655) hydrogen bonds : angle 6.47513 / 4.54 ( 1773) link_BETA1-4 : bond 0.00570 / 0.26 ( 8) link_BETA1-4 : angle 2.43578 / 1.64 ( 24) link_NAG-ASN : bond 0.00751 / 0.43 ( 12) link_NAG-ASN : angle 2.70194 / 1.80 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 0.711 Fit side-chains REVERT: D 220 ARG cc_start: 0.8581 (mmt90) cc_final: 0.7925 (mmt90) REVERT: D 287 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8004 (mt-10) REVERT: D 293 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7632 (ttp-170) REVERT: D 430 ARG cc_start: 0.8262 (mtm180) cc_final: 0.8023 (mtm180) REVERT: E 220 ARG cc_start: 0.8634 (mmt90) cc_final: 0.8015 (mmt90) REVERT: E 287 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7948 (mt-10) REVERT: E 430 ARG cc_start: 0.8353 (mtp-110) cc_final: 0.8123 (mmm160) REVERT: E 434 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7778 (m-40) REVERT: F 220 ARG cc_start: 0.8607 (mmt90) cc_final: 0.7863 (mmt90) REVERT: F 287 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8050 (mt-10) REVERT: F 293 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7108 (ttm170) REVERT: F 390 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8537 (tttt) REVERT: F 430 ARG cc_start: 0.8345 (mtm180) cc_final: 0.8118 (mtm180) REVERT: H 5 GLN cc_start: 0.7420 (tt0) cc_final: 0.6941 (tm-30) REVERT: H 74 SER cc_start: 0.7982 (p) cc_final: 0.7579 (t) REVERT: H 79 TYR cc_start: 0.8691 (m-80) cc_final: 0.8443 (m-80) REVERT: I 5 GLN cc_start: 0.7446 (tt0) cc_final: 0.6848 (mm-40) REVERT: I 7 SER cc_start: 0.7576 (p) cc_final: 0.7325 (m) REVERT: I 74 SER cc_start: 0.7980 (p) cc_final: 0.7559 (t) REVERT: J 5 GLN cc_start: 0.7496 (tt0) cc_final: 0.6870 (tm-30) REVERT: J 74 SER cc_start: 0.7923 (p) cc_final: 0.7463 (t) REVERT: K 220 ARG cc_start: 0.8632 (mmt90) cc_final: 0.7924 (mmt90) REVERT: K 287 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8078 (mt-10) REVERT: O 5 GLN cc_start: 0.7315 (tt0) cc_final: 0.6882 (mm-40) outliers start: 62 outliers final: 26 residues processed: 281 average time/residue: 0.5117 time to fit residues: 165.0708 Evaluate side-chains 244 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 434 ASN Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 118 ARG Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 293 ARG Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 390 LYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 355 ASN Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain P residue 50 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 83 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 369 ASN E 369 ASN E 449 ASN F 369 ASN F 449 ASN H 77 GLN I 77 GLN N 93 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.107468 restraints weight = 18250.631| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.38 r_work: 0.3009 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 19972 Z= 0.243 Angle : 0.769 9.577 27232 Z= 0.407 Chirality : 0.053 0.171 2984 Planarity : 0.006 0.060 3472 Dihedral : 7.220 59.142 3116 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 3.27 % Allowed : 11.45 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.16), residues: 2460 helix: -1.32 (0.95), residues: 24 sheet: 0.10 (0.16), residues: 1004 loop : -0.60 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 293 TYR 0.014 0.002 TYR E 253 PHE 0.030 0.003 PHE I 78 TRP 0.014 0.003 TRP K 97 HIS 0.005 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (19940) covalent geometry : angle 0.75992 / 0.41 (27148) SS BOND : bond 0.00376 / 0.22 ( 12) SS BOND : angle 1.21148 / 0.74 ( 24) hydrogen bonds : bond 0.05097 / 3.48 ( 655) hydrogen bonds : angle 6.41302 / 4.49 ( 1773) link_BETA1-4 : bond 0.00553 / 0.25 ( 8) link_BETA1-4 : angle 2.22275 / 1.52 ( 24) link_NAG-ASN : bond 0.00626 / 0.34 ( 12) link_NAG-ASN : angle 2.65085 / 1.71 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 214 time to evaluate : 0.642 Fit side-chains REVERT: D 220 ARG cc_start: 0.8599 (mmt90) cc_final: 0.7933 (mmt90) REVERT: D 430 ARG cc_start: 0.8277 (mtm180) cc_final: 0.7996 (mtm180) REVERT: E 220 ARG cc_start: 0.8636 (mmt90) cc_final: 0.7875 (mmt90) REVERT: E 287 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7889 (mt-10) REVERT: E 430 ARG cc_start: 0.8361 (mtp-110) cc_final: 0.8123 (mmm160) REVERT: E 434 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7713 (m-40) REVERT: F 220 ARG cc_start: 0.8589 (mmt90) cc_final: 0.7825 (mmt90) REVERT: F 293 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7043 (ttm170) REVERT: F 430 ARG cc_start: 0.8366 (mtm180) cc_final: 0.8007 (mtm180) REVERT: H 5 GLN cc_start: 0.7376 (tt0) cc_final: 0.6838 (tm-30) REVERT: H 74 SER cc_start: 0.7939 (p) cc_final: 0.7521 (t) REVERT: I 5 GLN cc_start: 0.7355 (tt0) cc_final: 0.6799 (mm-40) REVERT: J 5 GLN cc_start: 0.7398 (tt0) cc_final: 0.6699 (mm-40) REVERT: J 74 SER cc_start: 0.7825 (p) cc_final: 0.7364 (t) REVERT: K 220 ARG cc_start: 0.8609 (mmt90) cc_final: 0.7773 (mmt90) REVERT: K 287 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7908 (mt-10) REVERT: K 387 PHE cc_start: 0.8659 (p90) cc_final: 0.8386 (p90) REVERT: O 5 GLN cc_start: 0.7327 (tt0) cc_final: 0.6836 (mm-40) outliers start: 70 outliers final: 43 residues processed: 272 average time/residue: 0.5287 time to fit residues: 164.5161 Evaluate side-chains 257 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 273 ASN Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 434 ASN Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 118 ARG Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 293 ARG Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 118 ARG Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 355 ASN Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 90 optimal weight: 0.7980 chunk 236 optimal weight: 0.0980 chunk 208 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 449 ASN E 449 ASN F 449 ASN H 76 ASN K 449 ASN P 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109805 restraints weight = 18002.230| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.42 r_work: 0.3038 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19972 Z= 0.137 Angle : 0.631 9.375 27232 Z= 0.334 Chirality : 0.047 0.158 2984 Planarity : 0.005 0.040 3472 Dihedral : 6.611 59.934 3116 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.89 % Favored : 96.95 % Rotamer: Outliers : 2.62 % Allowed : 12.43 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2460 helix: -0.75 (0.96), residues: 24 sheet: 0.27 (0.16), residues: 996 loop : -0.45 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 430 TYR 0.010 0.001 TYR E 253 PHE 0.020 0.002 PHE H 78 TRP 0.013 0.002 TRP F 179 HIS 0.003 0.001 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (19940) covalent geometry : angle 0.62381 / 0.33 (27148) SS BOND : bond 0.00218 / 0.12 ( 12) SS BOND : angle 0.68726 / 0.44 ( 24) hydrogen bonds : bond 0.04220 / 2.88 ( 655) hydrogen bonds : angle 6.11085 / 4.28 ( 1773) link_BETA1-4 : bond 0.00513 / 0.24 ( 8) link_BETA1-4 : angle 1.80167 / 1.23 ( 24) link_NAG-ASN : bond 0.00422 / 0.24 ( 12) link_NAG-ASN : angle 2.32363 / 1.52 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 0.724 Fit side-chains REVERT: D 220 ARG cc_start: 0.8585 (mmt90) cc_final: 0.7941 (mmt90) REVERT: D 287 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7805 (mt-10) REVERT: D 293 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.6742 (ttm170) REVERT: D 430 ARG cc_start: 0.8221 (mtm180) cc_final: 0.7956 (mtm180) REVERT: E 287 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7904 (mt-10) REVERT: E 387 PHE cc_start: 0.8621 (p90) cc_final: 0.8388 (p90) REVERT: E 430 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.8085 (mmm160) REVERT: E 434 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7781 (m-40) REVERT: F 220 ARG cc_start: 0.8561 (mmt90) cc_final: 0.7851 (mmt90) REVERT: F 293 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.6851 (ttm170) REVERT: F 430 ARG cc_start: 0.8324 (mtm180) cc_final: 0.8016 (mtm180) REVERT: H 5 GLN cc_start: 0.7395 (tt0) cc_final: 0.6873 (tm-30) REVERT: H 74 SER cc_start: 0.7755 (p) cc_final: 0.7401 (t) REVERT: I 5 GLN cc_start: 0.7308 (tt0) cc_final: 0.6744 (mm-40) REVERT: I 74 SER cc_start: 0.7851 (p) cc_final: 0.7471 (t) REVERT: J 5 GLN cc_start: 0.7412 (tt0) cc_final: 0.6756 (mm-40) REVERT: J 74 SER cc_start: 0.7698 (p) cc_final: 0.7287 (t) REVERT: K 228 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: K 287 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7863 (mt-10) REVERT: O 5 GLN cc_start: 0.7320 (tt0) cc_final: 0.6809 (mm-40) outliers start: 56 outliers final: 30 residues processed: 268 average time/residue: 0.5218 time to fit residues: 160.4350 Evaluate side-chains 239 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 273 ASN Chi-restraints excluded: chain E residue 434 ASN Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 293 ARG Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 355 ASN Chi-restraints excluded: chain K residue 449 ASN Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 211 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 229 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 239 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 449 ASN E 273 ASN E 449 ASN F 449 ASN H 76 ASN J 76 ASN K 449 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113699 restraints weight = 17982.250| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.35 r_work: 0.3099 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19972 Z= 0.104 Angle : 0.563 9.102 27232 Z= 0.296 Chirality : 0.045 0.150 2984 Planarity : 0.004 0.033 3472 Dihedral : 5.883 57.147 3116 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % Rotamer: Outliers : 2.38 % Allowed : 13.27 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2460 helix: -0.28 (1.03), residues: 24 sheet: 0.38 (0.16), residues: 964 loop : -0.28 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 430 TYR 0.009 0.001 TYR E 253 PHE 0.015 0.002 PHE H 78 TRP 0.011 0.001 TRP O 47 HIS 0.003 0.001 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (19940) covalent geometry : angle 0.55704 / 0.29 (27148) SS BOND : bond 0.00209 / 0.12 ( 12) SS BOND : angle 0.54105 / 0.36 ( 24) hydrogen bonds : bond 0.03617 / 2.47 ( 655) hydrogen bonds : angle 5.79665 / 4.07 ( 1773) link_BETA1-4 : bond 0.00508 / 0.24 ( 8) link_BETA1-4 : angle 1.41430 / 0.95 ( 24) link_NAG-ASN : bond 0.00366 / 0.21 ( 12) link_NAG-ASN : angle 2.01168 / 1.30 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 0.500 Fit side-chains REVERT: D 220 ARG cc_start: 0.8498 (mmt90) cc_final: 0.7805 (mmt90) REVERT: D 293 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.6625 (ttm170) REVERT: D 378 ASN cc_start: 0.8477 (p0) cc_final: 0.8145 (p0) REVERT: E 287 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7815 (mt-10) REVERT: E 434 ASN cc_start: 0.8176 (t0) cc_final: 0.7809 (t0) REVERT: F 220 ARG cc_start: 0.8473 (mmt90) cc_final: 0.7716 (mmt90) REVERT: F 293 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.6745 (ttm170) REVERT: H 5 GLN cc_start: 0.7380 (tt0) cc_final: 0.6908 (mm-40) REVERT: H 74 SER cc_start: 0.7720 (p) cc_final: 0.7403 (t) REVERT: H 107 THR cc_start: 0.7902 (m) cc_final: 0.7496 (p) REVERT: I 5 GLN cc_start: 0.7275 (tt0) cc_final: 0.6672 (mm-40) REVERT: I 7 SER cc_start: 0.7749 (p) cc_final: 0.7427 (m) REVERT: I 74 SER cc_start: 0.7831 (p) cc_final: 0.7496 (t) REVERT: I 107 THR cc_start: 0.7854 (m) cc_final: 0.7454 (p) REVERT: J 5 GLN cc_start: 0.7390 (tt0) cc_final: 0.6762 (mm-40) REVERT: J 74 SER cc_start: 0.7689 (p) cc_final: 0.7322 (t) REVERT: K 228 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.6993 (tm-30) REVERT: O 5 GLN cc_start: 0.7317 (tt0) cc_final: 0.6806 (mm-40) REVERT: O 74 SER cc_start: 0.7812 (p) cc_final: 0.7506 (t) outliers start: 51 outliers final: 28 residues processed: 270 average time/residue: 0.5157 time to fit residues: 159.8443 Evaluate side-chains 239 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 293 ARG Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 242 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 162 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 225 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 449 ASN E 449 ASN F 449 ASN H 76 ASN I 76 ASN J 76 ASN K 449 ASN N 93 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111565 restraints weight = 17995.865| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.42 r_work: 0.3069 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19972 Z= 0.114 Angle : 0.574 7.654 27232 Z= 0.303 Chirality : 0.046 0.151 2984 Planarity : 0.004 0.032 3472 Dihedral : 5.726 57.921 3116 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.24 % Favored : 97.60 % Rotamer: Outliers : 2.29 % Allowed : 14.07 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.17), residues: 2460 helix: -0.14 (1.07), residues: 24 sheet: 0.43 (0.16), residues: 964 loop : -0.24 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 293 TYR 0.009 0.001 TYR D 253 PHE 0.019 0.002 PHE H 78 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (19940) covalent geometry : angle 0.56802 / 0.30 (27148) SS BOND : bond 0.00195 / 0.11 ( 12) SS BOND : angle 0.57054 / 0.36 ( 24) hydrogen bonds : bond 0.03802 / 2.60 ( 655) hydrogen bonds : angle 5.83378 / 4.09 ( 1773) link_BETA1-4 : bond 0.00492 / 0.23 ( 8) link_BETA1-4 : angle 1.33615 / 0.89 ( 24) link_NAG-ASN : bond 0.00335 / 0.19 ( 12) link_NAG-ASN : angle 2.08114 / 1.35 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 213 time to evaluate : 0.864 Fit side-chains REVERT: D 220 ARG cc_start: 0.8536 (mmt90) cc_final: 0.7833 (mmt90) REVERT: D 293 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.6702 (ttm170) REVERT: D 378 ASN cc_start: 0.8528 (p0) cc_final: 0.8195 (p0) REVERT: E 287 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7792 (mt-10) REVERT: E 434 ASN cc_start: 0.8183 (t0) cc_final: 0.7812 (t0) REVERT: F 220 ARG cc_start: 0.8511 (mmt90) cc_final: 0.7749 (mmt90) REVERT: F 293 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.6810 (ttm170) REVERT: F 430 ARG cc_start: 0.8234 (mtm180) cc_final: 0.7962 (mtm180) REVERT: H 5 GLN cc_start: 0.7390 (tt0) cc_final: 0.6908 (mm-40) REVERT: H 74 SER cc_start: 0.7719 (p) cc_final: 0.7402 (t) REVERT: H 107 THR cc_start: 0.7910 (m) cc_final: 0.7501 (p) REVERT: I 5 GLN cc_start: 0.7286 (tt0) cc_final: 0.6697 (mm-40) REVERT: I 7 SER cc_start: 0.7809 (p) cc_final: 0.7442 (m) REVERT: I 74 SER cc_start: 0.7794 (p) cc_final: 0.7461 (t) REVERT: I 107 THR cc_start: 0.7862 (m) cc_final: 0.7454 (p) REVERT: J 5 GLN cc_start: 0.7400 (tt0) cc_final: 0.6785 (mm-40) REVERT: J 74 SER cc_start: 0.7786 (p) cc_final: 0.7419 (t) REVERT: K 228 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: O 5 GLN cc_start: 0.7259 (tt0) cc_final: 0.6750 (mm-40) REVERT: O 74 SER cc_start: 0.7773 (p) cc_final: 0.7507 (t) outliers start: 49 outliers final: 30 residues processed: 250 average time/residue: 0.5407 time to fit residues: 154.7538 Evaluate side-chains 241 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 293 ARG Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 118 ARG Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 355 ASN Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 222 optimal weight: 40.0000 chunk 92 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 449 ASN E 449 ASN F 449 ASN H 76 ASN K 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.144740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.109403 restraints weight = 18007.579| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.42 r_work: 0.3032 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19972 Z= 0.157 Angle : 0.631 7.549 27232 Z= 0.335 Chirality : 0.048 0.154 2984 Planarity : 0.005 0.033 3472 Dihedral : 6.036 59.848 3116 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.01 % Favored : 96.83 % Rotamer: Outliers : 2.34 % Allowed : 14.02 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2460 helix: -0.20 (1.05), residues: 24 sheet: 0.43 (0.16), residues: 960 loop : -0.30 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 293 TYR 0.011 0.002 TYR E 253 PHE 0.023 0.002 PHE I 78 TRP 0.012 0.002 TRP F 97 HIS 0.003 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (19940) covalent geometry : angle 0.62514 / 0.33 (27148) SS BOND : bond 0.00211 / 0.12 ( 12) SS BOND : angle 0.78245 / 0.48 ( 24) hydrogen bonds : bond 0.04314 / 2.95 ( 655) hydrogen bonds : angle 6.05203 / 4.24 ( 1773) link_BETA1-4 : bond 0.00492 / 0.23 ( 8) link_BETA1-4 : angle 1.28968 / 0.84 ( 24) link_NAG-ASN : bond 0.00443 / 0.24 ( 12) link_NAG-ASN : angle 2.29497 / 1.50 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 0.616 Fit side-chains REVERT: D 220 ARG cc_start: 0.8607 (mmt90) cc_final: 0.7931 (mmt90) REVERT: D 293 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.6954 (ttm170) REVERT: D 378 ASN cc_start: 0.8571 (p0) cc_final: 0.8223 (p0) REVERT: E 287 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7836 (mt-10) REVERT: E 387 PHE cc_start: 0.8618 (p90) cc_final: 0.8358 (p90) REVERT: E 434 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7790 (m110) REVERT: F 220 ARG cc_start: 0.8581 (mmt90) cc_final: 0.7857 (mmt90) REVERT: F 293 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.6993 (ttm170) REVERT: H 5 GLN cc_start: 0.7332 (tt0) cc_final: 0.6829 (tm-30) REVERT: H 74 SER cc_start: 0.7710 (p) cc_final: 0.7387 (t) REVERT: H 107 THR cc_start: 0.7920 (m) cc_final: 0.7485 (p) REVERT: I 5 GLN cc_start: 0.7291 (tt0) cc_final: 0.6720 (mm-40) REVERT: I 7 SER cc_start: 0.7872 (p) cc_final: 0.7511 (m) REVERT: I 74 SER cc_start: 0.7813 (p) cc_final: 0.7481 (t) REVERT: J 5 GLN cc_start: 0.7374 (tt0) cc_final: 0.6751 (mm-40) REVERT: J 74 SER cc_start: 0.7800 (p) cc_final: 0.7439 (t) REVERT: O 5 GLN cc_start: 0.7253 (tt0) cc_final: 0.6774 (tm-30) REVERT: O 74 SER cc_start: 0.7772 (p) cc_final: 0.7500 (t) outliers start: 50 outliers final: 34 residues processed: 260 average time/residue: 0.5468 time to fit residues: 162.2109 Evaluate side-chains 257 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 434 ASN Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 293 ARG Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain K residue 118 ARG Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 355 ASN Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 208 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 115 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 449 ASN E 449 ASN F 449 ASN H 76 ASN K 449 ASN N 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111543 restraints weight = 17943.202| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.35 r_work: 0.3068 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19972 Z= 0.126 Angle : 0.591 8.030 27232 Z= 0.312 Chirality : 0.046 0.145 2984 Planarity : 0.004 0.032 3472 Dihedral : 5.814 58.879 3116 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.36 % Favored : 97.48 % Rotamer: Outliers : 2.20 % Allowed : 14.16 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.16), residues: 2460 helix: -0.28 (1.03), residues: 24 sheet: 0.40 (0.17), residues: 940 loop : -0.21 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 293 TYR 0.010 0.001 TYR D 253 PHE 0.020 0.002 PHE I 78 TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (19940) covalent geometry : angle 0.58537 / 0.31 (27148) SS BOND : bond 0.00207 / 0.12 ( 12) SS BOND : angle 0.64626 / 0.41 ( 24) hydrogen bonds : bond 0.03939 / 2.69 ( 655) hydrogen bonds : angle 5.92564 / 4.15 ( 1773) link_BETA1-4 : bond 0.00505 / 0.24 ( 8) link_BETA1-4 : angle 1.21525 / 0.80 ( 24) link_NAG-ASN : bond 0.00362 / 0.20 ( 12) link_NAG-ASN : angle 2.15302 / 1.39 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.650 Fit side-chains REVERT: D 220 ARG cc_start: 0.8562 (mmt90) cc_final: 0.7920 (mmt90) REVERT: D 293 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.6846 (ttm170) REVERT: D 378 ASN cc_start: 0.8497 (p0) cc_final: 0.8155 (p0) REVERT: E 287 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7799 (mt-10) REVERT: E 387 PHE cc_start: 0.8617 (p90) cc_final: 0.8366 (p90) REVERT: E 434 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7782 (m110) REVERT: F 220 ARG cc_start: 0.8540 (mmt90) cc_final: 0.7834 (mmt90) REVERT: F 293 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.6808 (ttm170) REVERT: F 430 ARG cc_start: 0.8205 (mtm180) cc_final: 0.7956 (mtm180) REVERT: H 5 GLN cc_start: 0.7357 (tt0) cc_final: 0.6847 (tm-30) REVERT: H 74 SER cc_start: 0.7691 (p) cc_final: 0.7422 (t) REVERT: H 107 THR cc_start: 0.7923 (m) cc_final: 0.7511 (p) REVERT: I 5 GLN cc_start: 0.7264 (tt0) cc_final: 0.6696 (mm-40) REVERT: I 7 SER cc_start: 0.7795 (p) cc_final: 0.7421 (m) REVERT: I 74 SER cc_start: 0.7830 (p) cc_final: 0.7514 (t) REVERT: I 107 THR cc_start: 0.7838 (m) cc_final: 0.7443 (p) REVERT: J 5 GLN cc_start: 0.7299 (tt0) cc_final: 0.6762 (mm-40) REVERT: J 74 SER cc_start: 0.7737 (p) cc_final: 0.7386 (t) REVERT: K 287 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: O 5 GLN cc_start: 0.7217 (tt0) cc_final: 0.6762 (mm-40) REVERT: O 74 SER cc_start: 0.7732 (p) cc_final: 0.7480 (t) outliers start: 47 outliers final: 35 residues processed: 250 average time/residue: 0.5520 time to fit residues: 157.8166 Evaluate side-chains 256 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 434 ASN Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 293 ARG Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain K residue 118 ARG Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 287 GLU Chi-restraints excluded: chain K residue 355 ASN Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 114 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 449 ASN E 449 ASN F 449 ASN H 76 ASN K 449 ASN N 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109890 restraints weight = 18097.571| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.42 r_work: 0.3039 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19972 Z= 0.140 Angle : 0.611 7.575 27232 Z= 0.324 Chirality : 0.047 0.149 2984 Planarity : 0.004 0.034 3472 Dihedral : 5.933 59.915 3116 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.76 % Favored : 97.07 % Rotamer: Outliers : 2.01 % Allowed : 14.49 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.16), residues: 2460 helix: -0.22 (1.04), residues: 24 sheet: 0.43 (0.17), residues: 936 loop : -0.23 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 293 TYR 0.010 0.001 TYR D 253 PHE 0.022 0.002 PHE I 78 TRP 0.011 0.002 TRP J 47 HIS 0.002 0.001 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (19940) covalent geometry : angle 0.60479 / 0.32 (27148) SS BOND : bond 0.00203 / 0.12 ( 12) SS BOND : angle 0.69328 / 0.42 ( 24) hydrogen bonds : bond 0.04170 / 2.85 ( 655) hydrogen bonds : angle 6.01982 / 4.22 ( 1773) link_BETA1-4 : bond 0.00481 / 0.22 ( 8) link_BETA1-4 : angle 1.17957 / 0.77 ( 24) link_NAG-ASN : bond 0.00392 / 0.22 ( 12) link_NAG-ASN : angle 2.24391 / 1.46 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 0.746 Fit side-chains REVERT: D 220 ARG cc_start: 0.8596 (mmt90) cc_final: 0.7937 (mmt90) REVERT: D 293 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.6928 (ttm170) REVERT: D 378 ASN cc_start: 0.8528 (p0) cc_final: 0.8171 (p0) REVERT: E 287 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7846 (mt-10) REVERT: E 387 PHE cc_start: 0.8620 (p90) cc_final: 0.8373 (p90) REVERT: E 434 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7788 (m110) REVERT: F 220 ARG cc_start: 0.8577 (mmt90) cc_final: 0.7847 (mmt90) REVERT: F 293 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.6964 (ttm170) REVERT: F 430 ARG cc_start: 0.8261 (mtm180) cc_final: 0.8004 (mtm180) REVERT: H 5 GLN cc_start: 0.7337 (tt0) cc_final: 0.6817 (tm-30) REVERT: H 74 SER cc_start: 0.7736 (p) cc_final: 0.7432 (t) REVERT: H 107 THR cc_start: 0.7916 (m) cc_final: 0.7487 (p) REVERT: I 5 GLN cc_start: 0.7246 (tt0) cc_final: 0.6709 (mm-40) REVERT: I 7 SER cc_start: 0.7846 (p) cc_final: 0.7471 (m) REVERT: I 74 SER cc_start: 0.7819 (p) cc_final: 0.7500 (t) REVERT: J 5 GLN cc_start: 0.7288 (tt0) cc_final: 0.6734 (mm-40) REVERT: J 74 SER cc_start: 0.7763 (p) cc_final: 0.7405 (t) REVERT: O 5 GLN cc_start: 0.7244 (tt0) cc_final: 0.6769 (mm-40) REVERT: O 74 SER cc_start: 0.7702 (p) cc_final: 0.7454 (t) outliers start: 43 outliers final: 33 residues processed: 252 average time/residue: 0.5308 time to fit residues: 152.8292 Evaluate side-chains 257 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 434 ASN Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 293 ARG Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain K residue 118 ARG Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 355 ASN Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 235 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 187 optimal weight: 0.0980 chunk 180 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 236 optimal weight: 0.2980 chunk 170 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 449 ASN E 449 ASN F 449 ASN H 76 ASN K 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.108554 restraints weight = 18090.767| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.43 r_work: 0.3014 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19972 Z= 0.177 Angle : 0.658 7.951 27232 Z= 0.349 Chirality : 0.048 0.147 2984 Planarity : 0.005 0.035 3472 Dihedral : 6.156 59.786 3116 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.03 % Rotamer: Outliers : 2.15 % Allowed : 14.35 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2460 helix: -0.46 (1.00), residues: 24 sheet: 0.37 (0.16), residues: 968 loop : -0.29 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 293 TYR 0.011 0.002 TYR D 253 PHE 0.026 0.003 PHE I 78 TRP 0.013 0.002 TRP F 97 HIS 0.003 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (19940) covalent geometry : angle 0.65124 / 0.35 (27148) SS BOND : bond 0.00251 / 0.14 ( 12) SS BOND : angle 0.92177 / 0.56 ( 24) hydrogen bonds : bond 0.04517 / 3.09 ( 655) hydrogen bonds : angle 6.15943 / 4.31 ( 1773) link_BETA1-4 : bond 0.00470 / 0.22 ( 8) link_BETA1-4 : angle 1.15534 / 0.74 ( 24) link_NAG-ASN : bond 0.00492 / 0.27 ( 12) link_NAG-ASN : angle 2.42069 / 1.58 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7115.73 seconds wall clock time: 122 minutes 8.44 seconds (7328.44 seconds total)