Starting phenix.real_space_refine on Fri Feb 6 08:49:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8i_62174/02_2026/9k8i_62174.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8i_62174/02_2026/9k8i_62174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k8i_62174/02_2026/9k8i_62174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8i_62174/02_2026/9k8i_62174.map" model { file = "/net/cci-nas-00/data/ceres_data/9k8i_62174/02_2026/9k8i_62174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8i_62174/02_2026/9k8i_62174.cif" } resolution = 3.16 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= 0.004 sd= 0.069 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 Zn 24 6.06 5 S 48 5.16 5 C 15324 2.51 5 N 3780 2.21 5 O 4596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23772 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} Chain: "B" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} Chain: "C" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} Chain: "D" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} Chain: "G" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} Chain: "J" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} Chain: "E" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} Chain: "H" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} Chain: "K" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} Chain: "F" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} Chain: "I" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} Chain: "L" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.91, per 1000 atoms: 0.21 Number of scatterers: 23772 At special positions: 0 Unit cell: (156.209, 147.59, 137.894, 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) Zn 24 29.99 S 48 16.00 O 4596 8.00 N 3780 7.00 C 15324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS B 64 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 51 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS J 247 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 240 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS C 64 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 51 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS F 247 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 240 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS A 64 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 51 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS E 247 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 240 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS G 64 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 51 " pdb=" ZN D 302 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS D 240 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS K 247 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 240 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS C 247 " pdb=" ZN E 302 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS H 64 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS E 51 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS B 247 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 240 " pdb=" ZN F 302 " pdb="ZN ZN F 302 " - pdb=" NE2 HIS I 64 " pdb="ZN ZN F 302 " - pdb=" NE2 HIS F 51 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS J 64 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 51 " pdb=" ZN G 302 " pdb="ZN ZN G 302 " - pdb=" NE2 HIS G 240 " pdb="ZN ZN G 302 " - pdb=" NE2 HIS I 247 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS K 64 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 51 " pdb=" ZN H 302 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS H 240 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS L 247 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 240 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS G 247 " pdb=" ZN I 302 " pdb="ZN ZN I 302 " - pdb=" NE2 HIS L 64 " pdb="ZN ZN I 302 " - pdb=" NE2 HIS I 51 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS A 247 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS J 240 " pdb=" ZN J 302 " pdb="ZN ZN J 302 " - pdb=" NE2 HIS D 64 " pdb="ZN ZN J 302 " - pdb=" NE2 HIS J 51 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS D 247 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 240 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" NE2 HIS E 64 " pdb="ZN ZN K 302 " - pdb=" NE2 HIS K 51 " pdb=" ZN L 301 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS H 247 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS L 240 " pdb=" ZN L 302 " pdb="ZN ZN L 302 " - pdb=" NE2 HIS F 64 " pdb="ZN ZN L 302 " - pdb=" NE2 HIS L 51 " 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 0 sheets defined 88.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 removed outlier: 3.843A pdb=" N ILE A 10 " --> pdb=" O MET A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 40 Processing helix chain 'A' and resid 43 through 60 removed outlier: 3.526A pdb=" N ASP A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 76 removed outlier: 3.763A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 98 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.578A pdb=" N GLU A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 removed outlier: 4.168A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 154 removed outlier: 4.014A pdb=" N LYS A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 178 removed outlier: 3.671A pdb=" N ILE A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.552A pdb=" N ALA A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.691A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 231 removed outlier: 3.552A pdb=" N ALA A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.512A pdb=" N ILE A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 19 Processing helix chain 'B' and resid 24 through 40 Processing helix chain 'B' and resid 43 through 60 Processing helix chain 'B' and resid 61 through 76 removed outlier: 3.816A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 98 Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.594A pdb=" N GLU B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 138 removed outlier: 4.200A pdb=" N VAL B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 154 removed outlier: 3.996A pdb=" N LYS B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.736A pdb=" N ILE B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.549A pdb=" N ALA B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.698A pdb=" N VAL B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 231 removed outlier: 3.514A pdb=" N ALA B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 251 removed outlier: 3.503A pdb=" N ILE B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 43 through 60 removed outlier: 3.629A pdb=" N ASP C 47 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 76 removed outlier: 3.767A pdb=" N ALA C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 98 Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.567A pdb=" N GLU C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 138 removed outlier: 4.158A pdb=" N VAL C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 155 removed outlier: 4.005A pdb=" N LYS C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 178 removed outlier: 3.662A pdb=" N ILE C 164 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.546A pdb=" N ALA C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.736A pdb=" N VAL C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 231 removed outlier: 3.578A pdb=" N ALA C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 251 removed outlier: 3.555A pdb=" N ILE C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 24 through 40 Processing helix chain 'D' and resid 43 through 60 removed outlier: 3.980A pdb=" N LEU D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 76 removed outlier: 3.801A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 98 Processing helix chain 'D' and resid 99 through 115 removed outlier: 3.588A pdb=" N GLU D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 138 removed outlier: 4.194A pdb=" N VAL D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 154 removed outlier: 4.008A pdb=" N LYS D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 178 removed outlier: 3.736A pdb=" N ILE D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.527A pdb=" N ALA D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.767A pdb=" N VAL D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 231 removed outlier: 3.536A pdb=" N ALA D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 251 removed outlier: 3.502A pdb=" N ILE D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 19 Processing helix chain 'G' and resid 24 through 40 Processing helix chain 'G' and resid 43 through 60 Processing helix chain 'G' and resid 61 through 76 removed outlier: 3.816A pdb=" N ALA G 65 " --> pdb=" O ASN G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 98 Processing helix chain 'G' and resid 99 through 115 removed outlier: 3.568A pdb=" N GLU G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 138 removed outlier: 4.188A pdb=" N VAL G 122 " --> pdb=" O ASP G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 154 removed outlier: 3.986A pdb=" N LYS G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 178 removed outlier: 3.645A pdb=" N ILE G 164 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY G 178 " --> pdb=" O LEU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 195 removed outlier: 3.532A pdb=" N ALA G 185 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY G 195 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 211 removed outlier: 3.759A pdb=" N VAL G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 231 removed outlier: 3.560A pdb=" N ALA G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 251 removed outlier: 3.516A pdb=" N ILE G 238 " --> pdb=" O ASP G 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS G 240 " --> pdb=" O GLU G 236 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET G 250 " --> pdb=" O GLU G 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 19 Processing helix chain 'J' and resid 24 through 40 Processing helix chain 'J' and resid 43 through 60 removed outlier: 3.522A pdb=" N ASP J 47 " --> pdb=" O ASP J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 76 removed outlier: 3.799A pdb=" N ALA J 65 " --> pdb=" O ASN J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 98 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.582A pdb=" N GLU J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 138 removed outlier: 4.178A pdb=" N VAL J 122 " --> pdb=" O ASP J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 154 removed outlier: 4.000A pdb=" N LYS J 144 " --> pdb=" O GLU J 140 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE J 145 " --> pdb=" O GLU J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 178 removed outlier: 3.763A pdb=" N ILE J 164 " --> pdb=" O VAL J 160 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU J 177 " --> pdb=" O LYS J 173 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY J 178 " --> pdb=" O LEU J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 195 removed outlier: 3.538A pdb=" N ALA J 185 " --> pdb=" O SER J 181 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY J 195 " --> pdb=" O LEU J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 210 removed outlier: 3.761A pdb=" N VAL J 201 " --> pdb=" O LEU J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 231 Processing helix chain 'J' and resid 234 through 251 removed outlier: 3.551A pdb=" N ILE J 238 " --> pdb=" O ASP J 234 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS J 240 " --> pdb=" O GLU J 236 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET J 250 " --> pdb=" O GLU J 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 43 through 60 removed outlier: 3.643A pdb=" N ASP E 47 " --> pdb=" O ASP E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 76 removed outlier: 3.850A pdb=" N ALA E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 98 Processing helix chain 'E' and resid 99 through 115 removed outlier: 3.590A pdb=" N GLU E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 138 removed outlier: 4.179A pdb=" N VAL E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 154 removed outlier: 4.007A pdb=" N LYS E 144 " --> pdb=" O GLU E 140 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE E 145 " --> pdb=" O GLU E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 178 removed outlier: 3.617A pdb=" N ILE E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 195 removed outlier: 3.536A pdb=" N ALA E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.722A pdb=" N VAL E 201 " --> pdb=" O LEU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 231 removed outlier: 3.565A pdb=" N ALA E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 251 removed outlier: 3.548A pdb=" N ILE E 238 " --> pdb=" O ASP E 234 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 19 Processing helix chain 'H' and resid 24 through 40 Processing helix chain 'H' and resid 43 through 60 removed outlier: 3.511A pdb=" N ASP H 47 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 76 removed outlier: 3.812A pdb=" N ALA H 65 " --> pdb=" O ASN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 98 Processing helix chain 'H' and resid 99 through 115 removed outlier: 3.582A pdb=" N GLU H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 138 removed outlier: 4.160A pdb=" N VAL H 122 " --> pdb=" O ASP H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 154 removed outlier: 4.009A pdb=" N LYS H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE H 145 " --> pdb=" O GLU H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 178 removed outlier: 3.753A pdb=" N ILE H 164 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY H 178 " --> pdb=" O LEU H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 195 removed outlier: 3.541A pdb=" N ALA H 185 " --> pdb=" O SER H 181 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY H 195 " --> pdb=" O LEU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 211 removed outlier: 3.696A pdb=" N VAL H 201 " --> pdb=" O LEU H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 231 removed outlier: 3.555A pdb=" N ALA H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 251 removed outlier: 3.516A pdb=" N ILE H 238 " --> pdb=" O ASP H 234 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS H 240 " --> pdb=" O GLU H 236 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET H 250 " --> pdb=" O GLU H 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 19 Processing helix chain 'K' and resid 24 through 40 Processing helix chain 'K' and resid 43 through 60 removed outlier: 3.570A pdb=" N ASP K 47 " --> pdb=" O ASP K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 76 removed outlier: 3.786A pdb=" N ALA K 65 " --> pdb=" O ASN K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 98 Processing helix chain 'K' and resid 99 through 115 removed outlier: 3.588A pdb=" N GLU K 115 " --> pdb=" O GLU K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 138 removed outlier: 4.208A pdb=" N VAL K 122 " --> pdb=" O ASP K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 154 removed outlier: 3.993A pdb=" N LYS K 144 " --> pdb=" O GLU K 140 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE K 145 " --> pdb=" O GLU K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 178 removed outlier: 3.722A pdb=" N ILE K 164 " --> pdb=" O VAL K 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU K 177 " --> pdb=" O LYS K 173 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY K 178 " --> pdb=" O LEU K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 195 removed outlier: 3.523A pdb=" N ALA K 185 " --> pdb=" O SER K 181 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY K 195 " --> pdb=" O LEU K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 211 removed outlier: 3.750A pdb=" N VAL K 201 " --> pdb=" O LEU K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 231 removed outlier: 3.518A pdb=" N ALA K 231 " --> pdb=" O LYS K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 251 removed outlier: 3.583A pdb=" N ILE K 238 " --> pdb=" O ASP K 234 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET K 250 " --> pdb=" O GLU K 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 19 Processing helix chain 'F' and resid 24 through 40 Processing helix chain 'F' and resid 43 through 60 removed outlier: 3.611A pdb=" N ASP F 47 " --> pdb=" O ASP F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 76 removed outlier: 3.840A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 98 Processing helix chain 'F' and resid 99 through 115 removed outlier: 3.582A pdb=" N GLU F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 138 removed outlier: 4.190A pdb=" N VAL F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 154 removed outlier: 3.996A pdb=" N LYS F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE F 145 " --> pdb=" O GLU F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 178 removed outlier: 3.636A pdb=" N ILE F 164 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY F 178 " --> pdb=" O LEU F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 195 removed outlier: 3.537A pdb=" N ALA F 185 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 removed outlier: 3.692A pdb=" N VAL F 201 " --> pdb=" O LEU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 231 removed outlier: 3.554A pdb=" N ALA F 231 " --> pdb=" O LYS F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 251 removed outlier: 3.523A pdb=" N ILE F 238 " --> pdb=" O ASP F 234 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET F 250 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 19 Processing helix chain 'I' and resid 24 through 40 Processing helix chain 'I' and resid 43 through 60 removed outlier: 4.002A pdb=" N LEU I 49 " --> pdb=" O GLU I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 76 removed outlier: 3.830A pdb=" N ALA I 65 " --> pdb=" O ASN I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 98 Processing helix chain 'I' and resid 99 through 115 removed outlier: 3.570A pdb=" N GLU I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 138 removed outlier: 4.181A pdb=" N VAL I 122 " --> pdb=" O ASP I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 154 removed outlier: 4.004A pdb=" N LYS I 144 " --> pdb=" O GLU I 140 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE I 145 " --> pdb=" O GLU I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 178 removed outlier: 3.699A pdb=" N ILE I 164 " --> pdb=" O VAL I 160 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU I 177 " --> pdb=" O LYS I 173 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY I 178 " --> pdb=" O LEU I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 195 removed outlier: 3.646A pdb=" N GLY I 195 " --> pdb=" O LEU I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 211 removed outlier: 3.781A pdb=" N VAL I 201 " --> pdb=" O LEU I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 231 removed outlier: 3.505A pdb=" N ALA I 231 " --> pdb=" O LYS I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 251 removed outlier: 3.524A pdb=" N ILE I 238 " --> pdb=" O ASP I 234 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS I 240 " --> pdb=" O GLU I 236 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET I 250 " --> pdb=" O GLU I 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 19 Processing helix chain 'L' and resid 24 through 40 Processing helix chain 'L' and resid 43 through 60 removed outlier: 3.718A pdb=" N LEU L 49 " --> pdb=" O GLU L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 76 removed outlier: 3.704A pdb=" N ALA L 65 " --> pdb=" O ASN L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 98 Processing helix chain 'L' and resid 99 through 115 removed outlier: 3.590A pdb=" N GLU L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 138 removed outlier: 4.182A pdb=" N VAL L 122 " --> pdb=" O ASP L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 154 removed outlier: 4.009A pdb=" N LYS L 144 " --> pdb=" O GLU L 140 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 178 removed outlier: 3.589A pdb=" N ILE L 164 " --> pdb=" O VAL L 160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU L 177 " --> pdb=" O LYS L 173 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY L 178 " --> pdb=" O LEU L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 195 removed outlier: 3.520A pdb=" N ALA L 185 " --> pdb=" O SER L 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY L 195 " --> pdb=" O LEU L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 211 removed outlier: 3.982A pdb=" N VAL L 201 " --> pdb=" O LEU L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 231 removed outlier: 3.599A pdb=" N ALA L 231 " --> pdb=" O LYS L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 251 removed outlier: 3.666A pdb=" N ILE L 238 " --> pdb=" O ASP L 234 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS L 240 " --> pdb=" O GLU L 236 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET L 250 " --> pdb=" O GLU L 246 " (cutoff:3.500A) 1840 hydrogen bonds defined for protein. 5520 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: 3.47 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4450 1.32 - 1.45: 4754 1.45 - 1.57: 14688 1.57 - 1.69: 0 1.69 - 1.82: 96 Bond restraints: 23988 Sorted by residual: bond pdb=" CA HIS A 247 " pdb=" C HIS A 247 " ideal model delta sigma weight residual 1.524 1.447 0.077 1.32e-02 5.74e+03 3.39e+01 bond pdb=" CA HIS J 247 " pdb=" C HIS J 247 " ideal model delta sigma weight residual 1.524 1.451 0.073 1.32e-02 5.74e+03 3.04e+01 bond pdb=" N HIS A 247 " pdb=" CA HIS A 247 " ideal model delta sigma weight residual 1.458 1.406 0.053 1.26e-02 6.30e+03 1.75e+01 bond pdb=" C GLU A 246 " pdb=" N HIS A 247 " ideal model delta sigma weight residual 1.334 1.279 0.055 1.43e-02 4.89e+03 1.49e+01 bond pdb=" C GLU J 246 " pdb=" N HIS J 247 " ideal model delta sigma weight residual 1.334 1.288 0.046 1.43e-02 4.89e+03 1.04e+01 ... (remaining 23983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 31657 2.08 - 4.16: 476 4.16 - 6.24: 71 6.24 - 8.32: 25 8.32 - 10.39: 3 Bond angle restraints: 32232 Sorted by residual: angle pdb=" N LEU I 130 " pdb=" CA LEU I 130 " pdb=" C LEU I 130 " ideal model delta sigma weight residual 111.28 104.93 6.35 1.09e+00 8.42e-01 3.40e+01 angle pdb=" N LEU G 130 " pdb=" CA LEU G 130 " pdb=" C LEU G 130 " ideal model delta sigma weight residual 111.28 105.04 6.24 1.09e+00 8.42e-01 3.28e+01 angle pdb=" N LEU E 130 " pdb=" CA LEU E 130 " pdb=" C LEU E 130 " ideal model delta sigma weight residual 111.36 105.62 5.74 1.09e+00 8.42e-01 2.77e+01 angle pdb=" C MET G 131 " pdb=" N ALA G 132 " pdb=" CA ALA G 132 " ideal model delta sigma weight residual 120.44 126.88 -6.44 1.30e+00 5.92e-01 2.45e+01 angle pdb=" C MET I 131 " pdb=" N ALA I 132 " pdb=" CA ALA I 132 " ideal model delta sigma weight residual 120.44 127.03 -6.59 1.36e+00 5.41e-01 2.35e+01 ... (remaining 32227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 12464 17.64 - 35.28: 1762 35.28 - 52.92: 662 52.92 - 70.57: 81 70.57 - 88.21: 7 Dihedral angle restraints: 14976 sinusoidal: 6252 harmonic: 8724 Sorted by residual: dihedral pdb=" CA GLY D 195 " pdb=" C GLY D 195 " pdb=" N ASP D 196 " pdb=" CA ASP D 196 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY K 195 " pdb=" C GLY K 195 " pdb=" N ASP K 196 " pdb=" CA ASP K 196 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA GLY J 195 " pdb=" C GLY J 195 " pdb=" N ASP J 196 " pdb=" CA ASP J 196 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 14973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2847 0.038 - 0.076: 867 0.076 - 0.114: 142 0.114 - 0.151: 7 0.151 - 0.189: 1 Chirality restraints: 3864 Sorted by residual: chirality pdb=" CA MET C 90 " pdb=" N MET C 90 " pdb=" C MET C 90 " pdb=" CB MET C 90 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA HIS J 247 " pdb=" N HIS J 247 " pdb=" C HIS J 247 " pdb=" CB HIS J 247 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA MET B 6 " pdb=" N MET B 6 " pdb=" C MET B 6 " pdb=" CB MET B 6 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 3861 not shown) Planarity restraints: 4032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 129 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C TYR E 129 " 0.042 2.00e-02 2.50e+03 pdb=" O TYR E 129 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU E 130 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 246 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C GLU A 246 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU A 246 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS A 247 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR G 129 " 0.012 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C TYR G 129 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR G 129 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU G 130 " 0.013 2.00e-02 2.50e+03 ... (remaining 4029 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 186 2.58 - 3.16: 19753 3.16 - 3.74: 38509 3.74 - 4.32: 49023 4.32 - 4.90: 82978 Nonbonded interactions: 190449 Sorted by model distance: nonbonded pdb=" OD1 ASP K 202 " pdb="ZN ZN K 301 " model vdw 1.999 2.230 nonbonded pdb=" OD1 ASP G 202 " pdb="ZN ZN G 302 " model vdw 2.002 2.230 nonbonded pdb=" OD1 ASP B 202 " pdb="ZN ZN B 302 " model vdw 2.007 2.230 nonbonded pdb=" OD1 ASP F 202 " pdb="ZN ZN F 301 " model vdw 2.014 2.230 nonbonded pdb=" OD1 ASP C 202 " pdb="ZN ZN C 302 " model vdw 2.023 2.230 ... (remaining 190444 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.830 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 22.700 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 0.314 24036 Z= 0.322 Angle : 0.668 10.394 32232 Z= 0.397 Chirality : 0.035 0.189 3864 Planarity : 0.002 0.024 4032 Dihedral : 18.019 88.208 9336 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.81 % Favored : 95.78 % Rotamer: Outliers : 0.16 % Allowed : 28.18 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.16), residues: 2964 helix: 1.42 (0.10), residues: 2484 sheet: None (None), residues: 0 loop : -2.09 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 76 TYR 0.009 0.001 TYR E 129 PHE 0.006 0.001 PHE H 149 HIS 0.011 0.001 HIS J 247 Details of bonding type rmsd covalent geometry : bond 0.00333 (23988) covalent geometry : angle 0.66812 (32232) hydrogen bonds : bond 0.15186 ( 1840) hydrogen bonds : angle 5.37134 ( 5520) metal coordination : bond 0.17494 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 203 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.9386 (mmm160) cc_final: 0.9073 (tpp-160) REVERT: A 121 TYR cc_start: 0.9089 (m-80) cc_final: 0.8782 (m-80) REVERT: B 29 ARG cc_start: 0.9380 (mmm160) cc_final: 0.9044 (tpp-160) REVERT: B 121 TYR cc_start: 0.9043 (m-80) cc_final: 0.8739 (m-80) REVERT: C 121 TYR cc_start: 0.9073 (m-80) cc_final: 0.8754 (m-80) REVERT: D 29 ARG cc_start: 0.9319 (mmm160) cc_final: 0.8951 (tpp-160) REVERT: D 121 TYR cc_start: 0.9075 (m-80) cc_final: 0.8690 (m-80) REVERT: G 121 TYR cc_start: 0.9062 (m-80) cc_final: 0.8637 (m-80) REVERT: J 121 TYR cc_start: 0.9008 (m-80) cc_final: 0.8705 (m-80) REVERT: E 121 TYR cc_start: 0.9098 (m-80) cc_final: 0.8665 (m-80) REVERT: H 121 TYR cc_start: 0.9052 (m-80) cc_final: 0.8586 (m-80) REVERT: K 29 ARG cc_start: 0.9369 (mmm160) cc_final: 0.9034 (tpp-160) REVERT: F 29 ARG cc_start: 0.9399 (mmm160) cc_final: 0.9072 (tpp-160) REVERT: F 121 TYR cc_start: 0.9102 (m-80) cc_final: 0.8721 (m-80) REVERT: I 29 ARG cc_start: 0.9316 (mmm160) cc_final: 0.8975 (tpp-160) REVERT: I 121 TYR cc_start: 0.9090 (m-80) cc_final: 0.8648 (m-80) REVERT: L 6 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8213 (ppp) REVERT: L 29 ARG cc_start: 0.9340 (mmm160) cc_final: 0.9016 (tpp-160) REVERT: L 121 TYR cc_start: 0.9053 (m-80) cc_final: 0.8782 (m-80) outliers start: 4 outliers final: 1 residues processed: 205 average time/residue: 0.2242 time to fit residues: 65.8384 Evaluate side-chains 152 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain L residue 6 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.052255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.041913 restraints weight = 141916.726| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 5.39 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24036 Z= 0.146 Angle : 0.562 9.648 32232 Z= 0.304 Chirality : 0.035 0.261 3864 Planarity : 0.003 0.034 4032 Dihedral : 4.325 53.831 3209 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.24 % Favored : 96.36 % Rotamer: Outliers : 2.24 % Allowed : 25.12 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.15), residues: 2964 helix: 1.59 (0.10), residues: 2580 sheet: None (None), residues: 0 loop : -3.02 (0.24), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 186 TYR 0.009 0.001 TYR F 150 PHE 0.016 0.001 PHE I 149 HIS 0.003 0.001 HIS J 51 Details of bonding type rmsd covalent geometry : bond 0.00326 (23988) covalent geometry : angle 0.56163 (32232) hydrogen bonds : bond 0.04193 ( 1840) hydrogen bonds : angle 4.14261 ( 5520) metal coordination : bond 0.00417 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 143 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.9419 (mmm160) cc_final: 0.9135 (mmm160) REVERT: A 121 TYR cc_start: 0.9099 (m-80) cc_final: 0.8849 (m-80) REVERT: A 223 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8772 (mp0) REVERT: B 29 ARG cc_start: 0.9440 (mmm160) cc_final: 0.9164 (mmm160) REVERT: B 121 TYR cc_start: 0.9075 (m-80) cc_final: 0.8750 (m-80) REVERT: B 223 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8736 (mp0) REVERT: C 29 ARG cc_start: 0.9430 (mmm160) cc_final: 0.9186 (mmm160) REVERT: D 121 TYR cc_start: 0.9024 (m-80) cc_final: 0.8661 (m-80) REVERT: G 121 TYR cc_start: 0.9060 (m-80) cc_final: 0.8672 (m-80) REVERT: G 131 MET cc_start: 0.8977 (ttm) cc_final: 0.8684 (mtp) REVERT: J 121 TYR cc_start: 0.9039 (m-80) cc_final: 0.8750 (m-80) REVERT: J 131 MET cc_start: 0.9051 (ptp) cc_final: 0.8849 (ptp) REVERT: E 29 ARG cc_start: 0.9400 (mmm160) cc_final: 0.9145 (mmm160) REVERT: E 121 TYR cc_start: 0.9045 (m-80) cc_final: 0.8657 (m-80) REVERT: H 121 TYR cc_start: 0.9082 (m-80) cc_final: 0.8595 (m-80) REVERT: K 121 TYR cc_start: 0.9065 (m-80) cc_final: 0.8814 (m-80) REVERT: F 29 ARG cc_start: 0.9427 (mmm160) cc_final: 0.9167 (mmm160) REVERT: F 50 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8687 (mm) REVERT: F 121 TYR cc_start: 0.9092 (m-80) cc_final: 0.8718 (m-80) REVERT: F 131 MET cc_start: 0.9065 (ptp) cc_final: 0.8830 (ptp) REVERT: I 121 TYR cc_start: 0.9092 (m-80) cc_final: 0.8637 (m-80) REVERT: L 121 TYR cc_start: 0.9094 (m-80) cc_final: 0.8802 (m-80) outliers start: 57 outliers final: 20 residues processed: 192 average time/residue: 0.2342 time to fit residues: 63.6916 Evaluate side-chains 151 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain D residue 6 MET Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain H residue 6 MET Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 184 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 264 optimal weight: 20.0000 chunk 218 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 240 optimal weight: 20.0000 chunk 282 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.051050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.040729 restraints weight = 142759.984| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 5.30 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24036 Z= 0.209 Angle : 0.614 9.696 32232 Z= 0.331 Chirality : 0.037 0.155 3864 Planarity : 0.003 0.030 4032 Dihedral : 4.497 44.842 3206 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.91 % Allowed : 25.35 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.15), residues: 2964 helix: 1.66 (0.10), residues: 2592 sheet: None (None), residues: 0 loop : -2.81 (0.23), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 186 TYR 0.010 0.002 TYR E 150 PHE 0.010 0.001 PHE I 149 HIS 0.003 0.001 HIS L 51 Details of bonding type rmsd covalent geometry : bond 0.00463 (23988) covalent geometry : angle 0.61358 (32232) hydrogen bonds : bond 0.04370 ( 1840) hydrogen bonds : angle 4.16577 ( 5520) metal coordination : bond 0.00415 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 134 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.9463 (mmm160) cc_final: 0.9185 (mmm160) REVERT: A 131 MET cc_start: 0.9097 (ptp) cc_final: 0.8881 (ptp) REVERT: B 29 ARG cc_start: 0.9464 (mmm160) cc_final: 0.9184 (mmm160) REVERT: C 29 ARG cc_start: 0.9466 (mmm160) cc_final: 0.9201 (mmm160) REVERT: D 131 MET cc_start: 0.9158 (ptp) cc_final: 0.8906 (ptp) REVERT: E 29 ARG cc_start: 0.9437 (mmm160) cc_final: 0.9175 (mmm160) REVERT: H 186 ARG cc_start: 0.9260 (mmm-85) cc_final: 0.8968 (mmm-85) REVERT: K 131 MET cc_start: 0.9160 (ptp) cc_final: 0.8932 (ptp) REVERT: K 216 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.9033 (pm20) REVERT: F 29 ARG cc_start: 0.9439 (mmm160) cc_final: 0.9176 (mmm160) REVERT: F 50 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8729 (mm) REVERT: I 50 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8671 (mm) REVERT: I 216 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8979 (pm20) outliers start: 74 outliers final: 30 residues processed: 196 average time/residue: 0.2434 time to fit residues: 67.8229 Evaluate side-chains 151 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 223 GLU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 216 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 133 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 183 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 99 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.051498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.041201 restraints weight = 141935.011| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 5.31 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24036 Z= 0.154 Angle : 0.560 10.066 32232 Z= 0.302 Chirality : 0.036 0.250 3864 Planarity : 0.003 0.034 4032 Dihedral : 4.257 31.468 3204 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.95 % Allowed : 24.92 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.15), residues: 2964 helix: 1.83 (0.10), residues: 2592 sheet: None (None), residues: 0 loop : -2.78 (0.23), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 186 TYR 0.009 0.001 TYR A 129 PHE 0.005 0.001 PHE I 149 HIS 0.002 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00352 (23988) covalent geometry : angle 0.56027 (32232) hydrogen bonds : bond 0.03956 ( 1840) hydrogen bonds : angle 3.92609 ( 5520) metal coordination : bond 0.00276 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 120 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.9434 (mmm160) cc_final: 0.9160 (mmm160) REVERT: A 131 MET cc_start: 0.9124 (ptp) cc_final: 0.8917 (ptp) REVERT: B 29 ARG cc_start: 0.9448 (mmm160) cc_final: 0.9174 (mmm160) REVERT: C 29 ARG cc_start: 0.9448 (mmm160) cc_final: 0.9177 (mmm160) REVERT: D 131 MET cc_start: 0.9190 (ptp) cc_final: 0.8988 (ptp) REVERT: D 186 ARG cc_start: 0.9346 (mmm160) cc_final: 0.9117 (mmm-85) REVERT: J 131 MET cc_start: 0.8962 (ptm) cc_final: 0.8420 (ptp) REVERT: E 29 ARG cc_start: 0.9412 (mmm160) cc_final: 0.9145 (mmm160) REVERT: E 133 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8987 (tt) REVERT: H 186 ARG cc_start: 0.9296 (mmm-85) cc_final: 0.8832 (mmm-85) REVERT: K 121 TYR cc_start: 0.9062 (m-80) cc_final: 0.8771 (m-80) REVERT: K 131 MET cc_start: 0.9192 (ptp) cc_final: 0.8968 (ptp) REVERT: K 216 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.9039 (pm20) REVERT: F 29 ARG cc_start: 0.9437 (mmm160) cc_final: 0.9161 (mmm160) REVERT: F 50 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8692 (mm) REVERT: F 131 MET cc_start: 0.8901 (ptm) cc_final: 0.8374 (ptp) REVERT: F 133 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9117 (tt) REVERT: I 50 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8620 (mm) REVERT: I 216 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.9019 (pm20) REVERT: L 206 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8592 (tp) outliers start: 75 outliers final: 30 residues processed: 187 average time/residue: 0.2318 time to fit residues: 62.2523 Evaluate side-chains 162 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 223 GLU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain H residue 6 MET Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 216 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 206 LEU Chi-restraints excluded: chain L residue 227 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 185 optimal weight: 0.0370 chunk 199 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.052077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.041878 restraints weight = 139972.907| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 5.30 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24036 Z= 0.115 Angle : 0.533 10.475 32232 Z= 0.283 Chirality : 0.035 0.281 3864 Planarity : 0.002 0.035 4032 Dihedral : 4.127 27.710 3204 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.87 % Allowed : 24.21 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.15), residues: 2964 helix: 2.05 (0.10), residues: 2592 sheet: None (None), residues: 0 loop : -2.68 (0.24), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 186 TYR 0.010 0.001 TYR A 129 PHE 0.003 0.001 PHE I 149 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd covalent geometry : bond 0.00264 (23988) covalent geometry : angle 0.53279 (32232) hydrogen bonds : bond 0.03546 ( 1840) hydrogen bonds : angle 3.68845 ( 5520) metal coordination : bond 0.00154 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 133 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.9411 (mmm160) cc_final: 0.9134 (mmm160) REVERT: A 131 MET cc_start: 0.9105 (ptp) cc_final: 0.8839 (ptp) REVERT: A 216 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.9057 (pm20) REVERT: B 29 ARG cc_start: 0.9439 (mmm160) cc_final: 0.9146 (mmm160) REVERT: D 131 MET cc_start: 0.9100 (ptp) cc_final: 0.8115 (ptp) REVERT: J 131 MET cc_start: 0.8923 (ptm) cc_final: 0.8303 (ptp) REVERT: E 29 ARG cc_start: 0.9385 (mmm160) cc_final: 0.9113 (mmm160) REVERT: E 133 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9022 (tt) REVERT: H 186 ARG cc_start: 0.9095 (mmm-85) cc_final: 0.8774 (mmm-85) REVERT: K 121 TYR cc_start: 0.9091 (m-80) cc_final: 0.8787 (m-80) REVERT: K 131 MET cc_start: 0.9153 (ptp) cc_final: 0.8842 (ptp) REVERT: F 29 ARG cc_start: 0.9411 (mmm160) cc_final: 0.9117 (mmm160) REVERT: F 50 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8687 (mm) REVERT: F 133 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9120 (tt) REVERT: I 50 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8573 (mm) outliers start: 73 outliers final: 32 residues processed: 198 average time/residue: 0.2291 time to fit residues: 65.3443 Evaluate side-chains 159 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 223 GLU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain H residue 6 MET Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 227 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 282 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 chunk 232 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.050896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.040692 restraints weight = 142106.438| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 5.28 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24036 Z= 0.185 Angle : 0.596 10.353 32232 Z= 0.315 Chirality : 0.036 0.233 3864 Planarity : 0.003 0.037 4032 Dihedral : 4.129 32.082 3204 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.75 % Allowed : 24.49 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.15), residues: 2964 helix: 2.02 (0.10), residues: 2592 sheet: None (None), residues: 0 loop : -2.67 (0.24), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 186 TYR 0.011 0.001 TYR C 150 PHE 0.005 0.001 PHE I 149 HIS 0.002 0.001 HIS K 51 Details of bonding type rmsd covalent geometry : bond 0.00415 (23988) covalent geometry : angle 0.59562 (32232) hydrogen bonds : bond 0.04007 ( 1840) hydrogen bonds : angle 3.89739 ( 5520) metal coordination : bond 0.00366 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 125 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.9425 (mmm160) cc_final: 0.9149 (mmm160) REVERT: B 29 ARG cc_start: 0.9463 (mmm160) cc_final: 0.9170 (mmm160) REVERT: D 43 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7635 (t0) REVERT: J 43 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7271 (t0) REVERT: J 131 MET cc_start: 0.9022 (ptm) cc_final: 0.8422 (ptp) REVERT: E 29 ARG cc_start: 0.9407 (mmm160) cc_final: 0.9127 (mmm160) REVERT: E 133 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9071 (tt) REVERT: H 186 ARG cc_start: 0.9146 (mmm-85) cc_final: 0.8846 (mmm-85) REVERT: K 131 MET cc_start: 0.9223 (ptp) cc_final: 0.8920 (ptp) REVERT: K 186 ARG cc_start: 0.8965 (mmm-85) cc_final: 0.8563 (mmm-85) REVERT: F 29 ARG cc_start: 0.9425 (mmm160) cc_final: 0.9156 (mmm160) REVERT: F 131 MET cc_start: 0.9080 (ptp) cc_final: 0.8030 (ptp) REVERT: F 133 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9237 (tt) REVERT: I 50 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8623 (mm) REVERT: I 216 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8993 (pm20) outliers start: 70 outliers final: 37 residues processed: 186 average time/residue: 0.2145 time to fit residues: 57.3333 Evaluate side-chains 164 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 43 ASP Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 223 GLU Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 227 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 210 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 chunk 171 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.058727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.048566 restraints weight = 121803.700| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 5.24 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24036 Z= 0.117 Angle : 0.561 10.509 32232 Z= 0.293 Chirality : 0.035 0.371 3864 Planarity : 0.003 0.039 4032 Dihedral : 4.083 28.300 3204 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.32 % Allowed : 24.49 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.15), residues: 2964 helix: 2.17 (0.10), residues: 2580 sheet: None (None), residues: 0 loop : -2.86 (0.24), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 186 TYR 0.012 0.001 TYR E 129 PHE 0.004 0.001 PHE A 102 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd covalent geometry : bond 0.00272 (23988) covalent geometry : angle 0.56075 (32232) hydrogen bonds : bond 0.03513 ( 1840) hydrogen bonds : angle 3.63119 ( 5520) metal coordination : bond 0.00171 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 127 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.9422 (mmm160) cc_final: 0.9138 (mmm160) REVERT: B 29 ARG cc_start: 0.9504 (mmm160) cc_final: 0.9220 (mmm160) REVERT: D 43 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7508 (t0) REVERT: G 141 GLU cc_start: 0.9564 (OUTLIER) cc_final: 0.9338 (pm20) REVERT: J 43 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7195 (t0) REVERT: J 131 MET cc_start: 0.9011 (ptm) cc_final: 0.8348 (ptp) REVERT: J 236 GLU cc_start: 0.9355 (OUTLIER) cc_final: 0.9084 (pm20) REVERT: E 29 ARG cc_start: 0.9387 (mmm160) cc_final: 0.9104 (mmm160) REVERT: E 133 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9067 (tt) REVERT: H 130 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9037 (mm) REVERT: K 131 MET cc_start: 0.9199 (ptp) cc_final: 0.8833 (ptp) REVERT: K 186 ARG cc_start: 0.8750 (mmm-85) cc_final: 0.8451 (mmm-85) REVERT: K 206 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8540 (tp) REVERT: F 29 ARG cc_start: 0.9441 (mmm160) cc_final: 0.9150 (mmm160) REVERT: F 50 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8668 (mm) REVERT: F 131 MET cc_start: 0.9050 (ptp) cc_final: 0.8665 (ptp) REVERT: F 133 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9143 (tt) REVERT: I 50 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8542 (mm) outliers start: 59 outliers final: 36 residues processed: 178 average time/residue: 0.2373 time to fit residues: 60.5308 Evaluate side-chains 172 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 43 ASP Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 223 GLU Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain H residue 6 MET Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 206 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 227 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 72 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 239 optimal weight: 7.9990 chunk 74 optimal weight: 0.0770 chunk 75 optimal weight: 6.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.058912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.048640 restraints weight = 121026.585| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 5.28 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24036 Z= 0.123 Angle : 0.566 10.521 32232 Z= 0.295 Chirality : 0.035 0.273 3864 Planarity : 0.002 0.032 4032 Dihedral : 3.981 26.321 3204 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.40 % Allowed : 24.37 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.15), residues: 2964 helix: 2.23 (0.10), residues: 2568 sheet: None (None), residues: 0 loop : -2.85 (0.24), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 186 TYR 0.010 0.001 TYR J 129 PHE 0.004 0.001 PHE A 102 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd covalent geometry : bond 0.00284 (23988) covalent geometry : angle 0.56573 (32232) hydrogen bonds : bond 0.03540 ( 1840) hydrogen bonds : angle 3.62841 ( 5520) metal coordination : bond 0.00196 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 129 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.9415 (mmm160) cc_final: 0.9127 (mmm160) REVERT: B 29 ARG cc_start: 0.9491 (mmm160) cc_final: 0.9201 (mmm160) REVERT: D 43 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7520 (t0) REVERT: G 141 GLU cc_start: 0.9569 (OUTLIER) cc_final: 0.9364 (pm20) REVERT: J 43 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7182 (t0) REVERT: J 131 MET cc_start: 0.9020 (ptm) cc_final: 0.8352 (ptp) REVERT: J 236 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.9009 (pm20) REVERT: E 29 ARG cc_start: 0.9387 (mmm160) cc_final: 0.9106 (mmm160) REVERT: E 133 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9044 (tt) REVERT: H 63 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.9069 (mp0) REVERT: H 131 MET cc_start: 0.9000 (ptp) cc_final: 0.8797 (ptp) REVERT: K 131 MET cc_start: 0.9206 (ptp) cc_final: 0.8825 (ptp) REVERT: K 186 ARG cc_start: 0.8757 (mmm-85) cc_final: 0.8468 (mmm-85) REVERT: K 206 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8537 (tp) REVERT: F 29 ARG cc_start: 0.9448 (mmm160) cc_final: 0.9155 (mmm160) REVERT: F 50 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8676 (mm) REVERT: F 131 MET cc_start: 0.9063 (ptp) cc_final: 0.8637 (ptp) REVERT: F 133 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9166 (tt) REVERT: I 50 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8505 (mm) REVERT: I 173 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9118 (tptp) outliers start: 61 outliers final: 33 residues processed: 181 average time/residue: 0.2451 time to fit residues: 63.0407 Evaluate side-chains 168 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 43 ASP Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain H residue 6 MET Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 206 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 173 LYS Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 227 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 148 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 257 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 189 optimal weight: 0.2980 chunk 177 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.059795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.049622 restraints weight = 121294.827| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 5.29 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24036 Z= 0.106 Angle : 0.569 10.848 32232 Z= 0.295 Chirality : 0.035 0.435 3864 Planarity : 0.002 0.036 4032 Dihedral : 3.908 24.325 3204 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.69 % Allowed : 24.84 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.15), residues: 2964 helix: 2.24 (0.10), residues: 2568 sheet: None (None), residues: 0 loop : -2.84 (0.24), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 186 TYR 0.011 0.001 TYR J 129 PHE 0.006 0.000 PHE A 102 HIS 0.002 0.000 HIS L 51 Details of bonding type rmsd covalent geometry : bond 0.00239 (23988) covalent geometry : angle 0.56877 (32232) hydrogen bonds : bond 0.03265 ( 1840) hydrogen bonds : angle 3.51534 ( 5520) metal coordination : bond 0.00083 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.9382 (mmm160) cc_final: 0.9097 (mmm160) REVERT: B 29 ARG cc_start: 0.9485 (mmm160) cc_final: 0.9196 (mmm160) REVERT: D 43 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7630 (t0) REVERT: G 141 GLU cc_start: 0.9562 (OUTLIER) cc_final: 0.9358 (pm20) REVERT: J 131 MET cc_start: 0.8899 (ptm) cc_final: 0.8207 (ptp) REVERT: J 236 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.9059 (pm20) REVERT: E 29 ARG cc_start: 0.9383 (mmm160) cc_final: 0.9095 (mmm160) REVERT: E 90 MET cc_start: 0.8791 (mtp) cc_final: 0.8585 (mtp) REVERT: E 133 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9099 (tt) REVERT: K 206 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8508 (tp) REVERT: F 29 ARG cc_start: 0.9435 (mmm160) cc_final: 0.9138 (mmm160) REVERT: F 50 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8692 (mm) REVERT: F 131 MET cc_start: 0.9050 (ptp) cc_final: 0.8586 (ptp) REVERT: F 133 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9064 (tt) REVERT: I 50 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8509 (mm) REVERT: I 173 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9129 (tptp) outliers start: 43 outliers final: 21 residues processed: 172 average time/residue: 0.2407 time to fit residues: 59.1564 Evaluate side-chains 163 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain H residue 6 MET Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 206 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 173 LYS Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 227 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 278 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 274 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 265 optimal weight: 9.9990 chunk 230 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.058055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.047801 restraints weight = 124997.162| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 5.30 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24036 Z= 0.149 Angle : 0.603 10.441 32232 Z= 0.313 Chirality : 0.037 0.416 3864 Planarity : 0.003 0.027 4032 Dihedral : 3.880 24.469 3204 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.81 % Allowed : 24.76 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.15), residues: 2964 helix: 2.27 (0.10), residues: 2568 sheet: None (None), residues: 0 loop : -2.81 (0.24), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 186 TYR 0.008 0.001 TYR J 150 PHE 0.007 0.001 PHE A 102 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd covalent geometry : bond 0.00341 (23988) covalent geometry : angle 0.60263 (32232) hydrogen bonds : bond 0.03711 ( 1840) hydrogen bonds : angle 3.69783 ( 5520) metal coordination : bond 0.00272 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.9414 (mmm160) cc_final: 0.9132 (mmm160) REVERT: B 29 ARG cc_start: 0.9511 (mmm160) cc_final: 0.9226 (mmm160) REVERT: C 250 MET cc_start: 0.8859 (ptm) cc_final: 0.8414 (ppp) REVERT: D 43 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7548 (t0) REVERT: G 141 GLU cc_start: 0.9581 (OUTLIER) cc_final: 0.9370 (pm20) REVERT: J 131 MET cc_start: 0.9000 (ptm) cc_final: 0.8385 (ptp) REVERT: J 236 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.9012 (pm20) REVERT: E 29 ARG cc_start: 0.9390 (mmm160) cc_final: 0.9103 (mmm160) REVERT: E 133 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9160 (tt) REVERT: H 63 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.9073 (mp0) REVERT: K 131 MET cc_start: 0.8997 (ptm) cc_final: 0.8739 (ptp) REVERT: K 206 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8529 (tp) REVERT: F 29 ARG cc_start: 0.9441 (mmm160) cc_final: 0.9149 (mmm160) REVERT: F 50 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8668 (mm) REVERT: F 131 MET cc_start: 0.9100 (ptp) cc_final: 0.8872 (ptp) REVERT: F 133 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9139 (tt) REVERT: I 50 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8576 (mm) REVERT: I 173 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9164 (tptp) REVERT: I 222 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8832 (mm) outliers start: 46 outliers final: 27 residues processed: 166 average time/residue: 0.2434 time to fit residues: 57.3114 Evaluate side-chains 165 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain H residue 6 MET Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 206 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 173 LYS Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 227 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 254 optimal weight: 0.5980 chunk 208 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.059124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.048892 restraints weight = 121834.777| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 5.32 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24036 Z= 0.118 Angle : 0.592 10.768 32232 Z= 0.306 Chirality : 0.036 0.393 3864 Planarity : 0.003 0.062 4032 Dihedral : 3.911 24.318 3204 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.65 % Allowed : 24.80 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.15), residues: 2964 helix: 2.26 (0.10), residues: 2568 sheet: None (None), residues: 0 loop : -2.82 (0.24), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 186 TYR 0.022 0.001 TYR G 150 PHE 0.006 0.001 PHE A 102 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd covalent geometry : bond 0.00275 (23988) covalent geometry : angle 0.59162 (32232) hydrogen bonds : bond 0.03492 ( 1840) hydrogen bonds : angle 3.59416 ( 5520) metal coordination : bond 0.00170 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4220.23 seconds wall clock time: 73 minutes 50.75 seconds (4430.75 seconds total)