Starting phenix.real_space_refine on Fri Aug 7 07:12:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ylu_73093/08_2026/9ylu_73093_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ylu_73093/08_2026/9ylu_73093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ylu_73093/08_2026/9ylu_73093_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ylu_73093/08_2026/9ylu_73093_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ylu_73093/08_2026/9ylu_73093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ylu_73093/08_2026/9ylu_73093.map" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 2 5.21 5 S 88 5.16 5 C 12227 2.51 5 N 3506 2.21 5 O 3803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19677 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2330 Classifications: {'peptide': 295} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 278} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2322 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 276} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2312 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 276} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2331 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 278} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2332 Classifications: {'peptide': 295} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 278} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2325 Classifications: {'peptide': 293} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 276} Chain: "G" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2302 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 273} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2326 Classifications: {'peptide': 295} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 278} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 383 Classifications: {'RNA': 18} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 360 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain: "K" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "L" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Chain: "M" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3} Link IDs: {'rna2p': 1, 'rna3p': 2} Chain: "N" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.44, per 1000 atoms: 0.23 Number of scatterers: 19677 At special positions: 0 Unit cell: (121.94, 140.7, 131.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 51 15.00 Mg 2 11.99 O 3803 8.00 N 3506 7.00 C 12227 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: 1.24 Conformation dependent library (CDL) restraints added in 650.4 milliseconds 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4338 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 28 sheets defined 42.8% alpha, 17.4% beta 9 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 removed outlier: 5.830A pdb=" N ASN A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.512A pdb=" N TYR A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 94 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.995A pdb=" N GLN A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 241 through 257 Processing helix chain 'A' and resid 283 through 296 Processing helix chain 'B' and resid 3 through 15 removed outlier: 5.636A pdb=" N ASN B 10 " --> pdb=" O ARG B 6 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TYR B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.642A pdb=" N TYR B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 95 Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.821A pdb=" N GLN B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 241 through 257 Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.732A pdb=" N GLU B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 removed outlier: 5.752A pdb=" N ASN C 10 " --> pdb=" O ARG C 6 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TYR C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 79 through 95 Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.913A pdb=" N GLN C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.505A pdb=" N ARG C 230 " --> pdb=" O PRO C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 257 Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'D' and resid 3 through 15 removed outlier: 5.870A pdb=" N ASN D 10 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 59 through 63 removed outlier: 3.584A pdb=" N ARG D 63 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 79 through 94 Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 177 through 189 Processing helix chain 'D' and resid 210 through 221 removed outlier: 3.977A pdb=" N GLN D 214 " --> pdb=" O SER D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 283 through 296 Processing helix chain 'E' and resid 3 through 15 removed outlier: 5.540A pdb=" N ASN E 10 " --> pdb=" O ARG E 6 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 59 through 63 Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 79 through 94 Processing helix chain 'E' and resid 153 through 161 Processing helix chain 'E' and resid 177 through 189 Processing helix chain 'E' and resid 210 through 221 removed outlier: 3.945A pdb=" N GLN E 214 " --> pdb=" O SER E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 241 through 257 Processing helix chain 'E' and resid 283 through 296 Processing helix chain 'F' and resid 3 through 15 removed outlier: 6.215A pdb=" N ASN F 10 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 79 through 94 Processing helix chain 'F' and resid 153 through 161 Processing helix chain 'F' and resid 177 through 189 Processing helix chain 'F' and resid 210 through 221 removed outlier: 3.798A pdb=" N GLN F 214 " --> pdb=" O SER F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 232 removed outlier: 3.666A pdb=" N ARG F 230 " --> pdb=" O PRO F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 257 Processing helix chain 'F' and resid 283 through 294 Processing helix chain 'G' and resid 5 through 15 removed outlier: 5.857A pdb=" N ASN G 10 " --> pdb=" O ARG G 6 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR G 11 " --> pdb=" O LEU G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 46 Processing helix chain 'G' and resid 59 through 63 Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 79 through 95 Processing helix chain 'G' and resid 153 through 161 Processing helix chain 'G' and resid 177 through 189 Processing helix chain 'G' and resid 210 through 221 removed outlier: 3.906A pdb=" N GLN G 214 " --> pdb=" O SER G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 241 through 257 Processing helix chain 'G' and resid 283 through 291 Processing helix chain 'H' and resid 3 through 15 removed outlier: 3.544A pdb=" N LEU H 7 " --> pdb=" O LYS H 3 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASN H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TYR H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 45 Processing helix chain 'H' and resid 59 through 63 Processing helix chain 'H' and resid 67 through 72 Processing helix chain 'H' and resid 79 through 94 Processing helix chain 'H' and resid 153 through 161 Processing helix chain 'H' and resid 177 through 189 Processing helix chain 'H' and resid 210 through 221 removed outlier: 3.988A pdb=" N GLN H 214 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS H 216 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 232 Processing helix chain 'H' and resid 241 through 257 Processing helix chain 'H' and resid 283 through 296 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24 removed outlier: 6.561A pdb=" N ASP A 22 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.671A pdb=" N ASP A 148 " --> pdb=" O ARG A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 196 removed outlier: 6.887A pdb=" N ARG A 167 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU A 194 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS A 261 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG A 266 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL A 277 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 21 through 24 Processing sheet with id=AA5, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.624A pdb=" N ASP B 148 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 196 removed outlier: 6.499A pdb=" N ARG B 167 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU B 196 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B 169 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE B 235 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE B 168 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASN B 237 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 170 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS B 261 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG B 266 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL B 277 " --> pdb=" O ARG B 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 24 removed outlier: 6.507A pdb=" N ASP C 22 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 142 through 144 Processing sheet with id=AA9, first strand: chain 'C' and resid 191 through 196 removed outlier: 6.058A pdb=" N ARG C 167 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 194 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE C 235 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE C 168 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN C 237 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU C 170 " --> pdb=" O ASN C 237 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS C 261 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG C 266 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL C 277 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.617A pdb=" N ASP D 22 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 95 through 96 Processing sheet with id=AB3, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.630A pdb=" N ASP D 148 " --> pdb=" O ARG D 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 191 through 196 removed outlier: 7.172A pdb=" N ARG D 167 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N LEU D 196 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 169 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE D 235 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE D 168 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASN D 237 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU D 170 " --> pdb=" O ASN D 237 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS D 261 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ARG D 266 " --> pdb=" O VAL D 277 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL D 277 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 21 through 24 removed outlier: 6.397A pdb=" N ASP E 22 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 Processing sheet with id=AB7, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.740A pdb=" N ASP E 148 " --> pdb=" O ARG E 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 191 through 196 removed outlier: 6.965A pdb=" N ARG E 167 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU E 194 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS E 261 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG E 266 " --> pdb=" O VAL E 277 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL E 277 " --> pdb=" O ARG E 266 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 21 through 24 Processing sheet with id=AC1, first strand: chain 'F' and resid 95 through 96 Processing sheet with id=AC2, first strand: chain 'F' and resid 142 through 144 Processing sheet with id=AC3, first strand: chain 'F' and resid 191 through 196 removed outlier: 5.981A pdb=" N ARG F 167 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU F 194 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS F 261 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG F 266 " --> pdb=" O VAL F 277 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL F 277 " --> pdb=" O ARG F 266 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 21 through 24 removed outlier: 6.515A pdb=" N ASP G 22 " --> pdb=" O ILE G 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.736A pdb=" N ASP G 148 " --> pdb=" O ARG G 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 191 through 196 removed outlier: 5.979A pdb=" N ARG G 167 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU G 194 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS G 261 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG G 266 " --> pdb=" O VAL G 277 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N VAL G 277 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 21 through 24 removed outlier: 3.535A pdb=" N GLY H 116 " --> pdb=" O ILE H 55 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 95 through 96 Processing sheet with id=AC9, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.981A pdb=" N ASP H 148 " --> pdb=" O ARG H 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 191 through 196 removed outlier: 7.008A pdb=" N ARG H 167 " --> pdb=" O GLU H 194 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU H 196 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL H 169 " --> pdb=" O LEU H 196 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE H 235 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE H 168 " --> pdb=" O ILE H 235 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASN H 237 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU H 170 " --> pdb=" O ASN H 237 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS H 261 " --> pdb=" O LEU H 234 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG H 266 " --> pdb=" O VAL H 277 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL H 277 " --> pdb=" O ARG H 266 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2424 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.60 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: 3248 1.32 - 1.44: 5215 1.44 - 1.57: 11429 1.57 - 1.69: 96 1.69 - 1.81: 152 Bond restraints: 20140 Sorted by residual: bond pdb=" N ASN C 96 " pdb=" CA ASN C 96 " ideal model delta sigma weight residual 1.463 1.492 -0.029 6.90e-03 2.10e+04 1.78e+01 bond pdb=" N ILE A 98 " pdb=" CA ILE A 98 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.50e-03 1.78e+04 1.76e+01 bond pdb=" N ILE G 101 " pdb=" CA ILE G 101 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.11e-02 8.12e+03 1.31e+01 bond pdb=" N GLY G 51 " pdb=" CA GLY G 51 " ideal model delta sigma weight residual 1.444 1.476 -0.032 9.30e-03 1.16e+04 1.22e+01 bond pdb=" N ILE G 47 " pdb=" CA ILE G 47 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.10e-02 8.26e+03 1.09e+01 ... (remaining 20135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 26483 1.63 - 3.27: 849 3.27 - 4.90: 139 4.90 - 6.53: 37 6.53 - 8.17: 8 Bond angle restraints: 27516 Sorted by residual: angle pdb=" CA THR B 46 " pdb=" CB THR B 46 " pdb=" OG1 THR B 46 " ideal model delta sigma weight residual 109.60 103.04 6.56 1.50e+00 4.44e-01 1.91e+01 angle pdb=" CA GLY C 116 " pdb=" C GLY C 116 " pdb=" O GLY C 116 " ideal model delta sigma weight residual 121.64 118.07 3.57 9.20e-01 1.18e+00 1.50e+01 angle pdb=" C3' A M 3 " pdb=" C2' A M 3 " pdb=" C1' A M 3 " ideal model delta sigma weight residual 101.50 104.52 -3.02 8.00e-01 1.56e+00 1.43e+01 angle pdb=" N LYS C 30 " pdb=" CA LYS C 30 " pdb=" C LYS C 30 " ideal model delta sigma weight residual 113.88 109.27 4.61 1.23e+00 6.61e-01 1.40e+01 angle pdb=" C3' A M 2 " pdb=" C2' A M 2 " pdb=" C1' A M 2 " ideal model delta sigma weight residual 101.30 103.90 -2.60 7.00e-01 2.04e+00 1.38e+01 ... (remaining 27511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 11838 35.99 - 71.98: 442 71.98 - 107.97: 33 107.97 - 143.97: 1 143.97 - 179.96: 5 Dihedral angle restraints: 12319 sinusoidal: 5583 harmonic: 6736 Sorted by residual: dihedral pdb=" O4' C J 6 " pdb=" C1' C J 6 " pdb=" N1 C J 6 " pdb=" C2 C J 6 " ideal model delta sinusoidal sigma weight residual -160.00 17.60 -177.60 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U J 7 " pdb=" C1' U J 7 " pdb=" N1 U J 7 " pdb=" C2 U J 7 " ideal model delta sinusoidal sigma weight residual 200.00 33.96 166.04 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" C5' A K 4 " pdb=" C4' A K 4 " pdb=" C3' A K 4 " pdb=" O3' A K 4 " ideal model delta sinusoidal sigma weight residual 147.00 88.68 58.32 1 8.00e+00 1.56e-02 7.12e+01 ... (remaining 12316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2982 0.115 - 0.229: 157 0.229 - 0.344: 1 0.344 - 0.459: 9 0.459 - 0.574: 11 Chirality restraints: 3160 Sorted by residual: chirality pdb=" P A M 1 " pdb=" OP1 A M 1 " pdb=" OP2 A M 1 " pdb=" O5' A M 1 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.23e+00 chirality pdb=" P A N 1 " pdb=" OP1 A N 1 " pdb=" OP2 A N 1 " pdb=" O5' A N 1 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" P A K 1 " pdb=" OP1 A K 1 " pdb=" OP2 A K 1 " pdb=" O5' A K 1 " both_signs ideal model delta sigma weight residual True 2.41 2.95 -0.54 2.00e-01 2.50e+01 7.22e+00 ... (remaining 3157 not shown) Planarity restraints: 3381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 94 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.81e+00 pdb=" C TYR A 94 " 0.048 2.00e-02 2.50e+03 pdb=" O TYR A 94 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS A 95 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 92 " 0.010 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C SER C 92 " -0.033 2.00e-02 2.50e+03 pdb=" O SER C 92 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN C 93 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 45 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C ASN B 45 " -0.028 2.00e-02 2.50e+03 pdb=" O ASN B 45 " 0.010 2.00e-02 2.50e+03 pdb=" N THR B 46 " 0.010 2.00e-02 2.50e+03 ... (remaining 3378 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 38 2.54 - 3.13: 14412 3.13 - 3.72: 30185 3.72 - 4.31: 45129 4.31 - 4.90: 74758 Nonbonded interactions: 164522 Sorted by model distance: nonbonded pdb=" OP1 U J 7 " pdb="MG MG C 301 " model vdw 1.956 2.170 nonbonded pdb=" O MET B 256 " pdb=" OG SER B 257 " model vdw 2.221 3.040 nonbonded pdb=" OE2 GLU C 17 " pdb="MG MG C 301 " model vdw 2.243 2.170 nonbonded pdb=" O LEU F 23 " pdb="MG MG F 301 " model vdw 2.281 2.170 nonbonded pdb=" O ASP B 135 " pdb=" OD1 ASP B 135 " model vdw 2.294 3.040 ... (remaining 164517 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 29 or (resid 30 and (name N or name \ CA or name C or name O )) or resid 31 through 99 or (resid 100 and (name N or n \ ame CA or name C or name O or name CB )) or resid 101 through 294)) selection = (chain 'B' and (resid 4 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 29 or (resid 30 and (name N or name \ CA or name C or name O )) or resid 31 through 99 or (resid 100 and (name N or n \ ame CA or name C or name O or name CB )) or resid 101 through 294)) selection = (chain 'C' and (resid 4 through 29 or (resid 30 and (name N or name CA or name C \ or name O )) or resid 31 through 294)) selection = (chain 'D' and (resid 4 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 29 or (resid 30 and (name N or name \ CA or name C or name O )) or resid 31 through 99 or (resid 100 and (name N or n \ ame CA or name C or name O or name CB )) or resid 101 through 294)) selection = (chain 'E' and (resid 4 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 29 or (resid 30 and (name N or name \ CA or name C or name O )) or resid 31 through 99 or (resid 100 and (name N or n \ ame CA or name C or name O or name CB )) or resid 101 through 294)) selection = (chain 'F' and (resid 4 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 29 or (resid 30 and (name N or name \ CA or name C or name O )) or resid 31 through 99 or (resid 100 and (name N or n \ ame CA or name C or name O or name CB )) or resid 101 through 294)) selection = (chain 'G' and (resid 4 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 29 or (resid 30 and (name N or name \ CA or name C or name O )) or resid 31 through 294)) selection = (chain 'H' and (resid 4 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 29 through 99 or (resid 100 and (na \ me N or name CA or name C or name O or name CB )) or resid 101 through 294)) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.410 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 : 0.004 0.045 20140 Z= 0.300 Angle : 0.676 8.168 27516 Z= 0.422 Chirality : 0.064 0.574 3160 Planarity : 0.004 0.043 3381 Dihedral : 17.400 179.957 7981 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 18.51 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 2334 helix: 1.65 (0.18), residues: 875 sheet: -0.21 (0.29), residues: 283 loop : -0.33 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 16 TYR 0.009 0.001 TYR C 71 PHE 0.006 0.001 PHE A 36 TRP 0.012 0.001 TRP E 5 HIS 0.002 0.000 HIS C 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.30 (20140) covalent geometry : angle 0.67635 / 0.42 (27516) hydrogen bonds : bond 0.13543 / 8.80 ( 870) hydrogen bonds : angle 6.31869 / 4.57 ( 2474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.659 Fit side-chains REVERT: A 61 LYS cc_start: 0.8625 (tttt) cc_final: 0.8177 (mmmm) REVERT: B 35 LYS cc_start: 0.8002 (mttp) cc_final: 0.7703 (mmtm) REVERT: D 81 ASP cc_start: 0.7873 (t70) cc_final: 0.7662 (t0) REVERT: E 141 MET cc_start: 0.8852 (mtm) cc_final: 0.8595 (mpp) REVERT: F 35 LYS cc_start: 0.8632 (mttp) cc_final: 0.8318 (mmtp) REVERT: F 289 LYS cc_start: 0.7441 (mptt) cc_final: 0.7191 (mptm) REVERT: G 186 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8233 (tm-30) REVERT: G 289 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7740 (tttt) REVERT: H 289 LYS cc_start: 0.8594 (mttt) cc_final: 0.8357 (mmtm) outliers start: 0 outliers final: 1 residues processed: 297 average time/residue: 0.7812 time to fit residues: 255.0381 Evaluate side-chains 270 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 179 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 GLN A 186 GLN B 178 GLN C 66 ASN D 186 GLN D 189 ASN E 186 GLN F 66 ASN G 93 ASN G 96 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.148448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103904 restraints weight = 23931.283| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.94 r_work: 0.3250 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20140 Z= 0.154 Angle : 0.543 10.130 27516 Z= 0.283 Chirality : 0.046 0.331 3160 Planarity : 0.005 0.057 3381 Dihedral : 13.623 178.531 3318 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.51 % Allowed : 17.09 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2334 helix: 2.01 (0.18), residues: 883 sheet: 0.18 (0.29), residues: 275 loop : -0.32 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 100 TYR 0.020 0.001 TYR C 71 PHE 0.010 0.001 PHE E 241 TRP 0.017 0.001 TRP E 5 HIS 0.004 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (20140) covalent geometry : angle 0.54275 / 0.28 (27516) hydrogen bonds : bond 0.04077 / 2.76 ( 870) hydrogen bonds : angle 5.06195 / 3.63 ( 2474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 0.772 Fit side-chains REVERT: A 58 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8543 (mm) REVERT: A 61 LYS cc_start: 0.8757 (tttt) cc_final: 0.8021 (mmmm) REVERT: A 274 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6263 (mp) REVERT: B 124 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8819 (mp) REVERT: B 148 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7488 (m-30) REVERT: B 165 ASP cc_start: 0.7908 (p0) cc_final: 0.7681 (p0) REVERT: B 289 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7774 (mttt) REVERT: C 141 MET cc_start: 0.9231 (mtm) cc_final: 0.8875 (mtm) REVERT: D 81 ASP cc_start: 0.7836 (t70) cc_final: 0.7614 (t0) REVERT: E 141 MET cc_start: 0.9232 (mtm) cc_final: 0.8947 (mpp) REVERT: E 216 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7689 (ttmm) REVERT: E 253 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: F 35 LYS cc_start: 0.8195 (mttp) cc_final: 0.7866 (mmtp) REVERT: F 289 LYS cc_start: 0.6888 (mptt) cc_final: 0.6679 (mptm) REVERT: G 158 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7423 (mtt180) REVERT: G 165 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.5996 (t0) REVERT: G 178 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6722 (mp10) REVERT: G 186 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7899 (tm-30) REVERT: H 35 LYS cc_start: 0.7853 (mttt) cc_final: 0.6991 (pttp) REVERT: H 61 LYS cc_start: 0.8457 (mmmm) cc_final: 0.7965 (mppt) REVERT: H 289 LYS cc_start: 0.8457 (mttt) cc_final: 0.7756 (mmtm) outliers start: 51 outliers final: 20 residues processed: 287 average time/residue: 0.7336 time to fit residues: 232.3858 Evaluate side-chains 283 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 4 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 232 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 58 optimal weight: 0.0870 chunk 179 optimal weight: 1.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 GLN A 186 GLN B 189 ASN C 214 GLN D 186 GLN D 189 ASN F 66 ASN G 253 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103704 restraints weight = 22539.256| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.07 r_work: 0.3128 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20140 Z= 0.140 Angle : 0.503 7.963 27516 Z= 0.262 Chirality : 0.045 0.208 3160 Planarity : 0.004 0.059 3381 Dihedral : 13.514 179.980 3316 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.41 % Allowed : 17.97 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.05 % 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: 1.14 (0.18), residues: 2334 helix: 2.18 (0.18), residues: 883 sheet: 0.62 (0.28), residues: 314 loop : -0.33 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 16 TYR 0.020 0.001 TYR C 71 PHE 0.012 0.001 PHE E 241 TRP 0.015 0.001 TRP E 5 HIS 0.003 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (20140) covalent geometry : angle 0.50305 / 0.26 (27516) hydrogen bonds : bond 0.03756 / 2.54 ( 870) hydrogen bonds : angle 4.82626 / 3.47 ( 2474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 265 time to evaluate : 0.735 Fit side-chains REVERT: A 22 ASP cc_start: 0.8244 (t70) cc_final: 0.7714 (t0) REVERT: A 61 LYS cc_start: 0.8844 (tttt) cc_final: 0.8098 (mmmm) REVERT: A 274 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6174 (mp) REVERT: B 24 LYS cc_start: 0.7432 (mtpp) cc_final: 0.6832 (mmtt) REVERT: B 124 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8842 (mp) REVERT: B 148 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: B 165 ASP cc_start: 0.7848 (p0) cc_final: 0.7607 (p0) REVERT: B 289 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7805 (mttt) REVERT: D 3 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7612 (pttm) REVERT: D 81 ASP cc_start: 0.7750 (t70) cc_final: 0.7541 (t0) REVERT: E 141 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8980 (mpp) REVERT: E 216 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7646 (ttmm) REVERT: E 253 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: F 35 LYS cc_start: 0.8242 (mttp) cc_final: 0.7934 (mmtp) REVERT: F 93 ASN cc_start: 0.8218 (t0) cc_final: 0.7847 (t0) REVERT: G 98 ILE cc_start: 0.6791 (mp) cc_final: 0.6574 (mp) REVERT: G 114 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.6304 (ptmm) REVERT: G 158 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7305 (mtt180) REVERT: G 165 ASP cc_start: 0.6389 (OUTLIER) cc_final: 0.5857 (t0) REVERT: G 178 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6797 (mp10) REVERT: G 186 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7904 (tm-30) REVERT: G 289 LYS cc_start: 0.7673 (ttmm) cc_final: 0.7239 (tttt) REVERT: H 35 LYS cc_start: 0.7754 (mttt) cc_final: 0.6942 (pttp) REVERT: H 60 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7593 (tt) REVERT: H 61 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8016 (mppt) REVERT: H 289 LYS cc_start: 0.8366 (mttt) cc_final: 0.7666 (mmtm) outliers start: 49 outliers final: 18 residues processed: 285 average time/residue: 0.7002 time to fit residues: 220.5838 Evaluate side-chains 285 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 131 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 224 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 95 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 146 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN B 189 ASN C 261 HIS D 186 GLN D 189 ASN E 186 GLN F 253 GLN G 253 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.149228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105058 restraints weight = 22513.252| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.09 r_work: 0.3144 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20140 Z= 0.103 Angle : 0.471 7.223 27516 Z= 0.246 Chirality : 0.044 0.195 3160 Planarity : 0.004 0.061 3381 Dihedral : 13.413 179.228 3316 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.76 % Allowed : 18.32 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.05 % 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: 1.24 (0.18), residues: 2334 helix: 2.33 (0.17), residues: 884 sheet: 0.43 (0.32), residues: 229 loop : -0.20 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 100 TYR 0.017 0.001 TYR C 71 PHE 0.007 0.001 PHE E 241 TRP 0.016 0.001 TRP E 5 HIS 0.002 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (20140) covalent geometry : angle 0.47129 / 0.25 (27516) hydrogen bonds : bond 0.03263 / 2.21 ( 870) hydrogen bonds : angle 4.67917 / 3.37 ( 2474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 0.831 Fit side-chains REVERT: A 22 ASP cc_start: 0.8186 (t70) cc_final: 0.7687 (t0) REVERT: A 58 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8366 (mm) REVERT: A 61 LYS cc_start: 0.8831 (tttt) cc_final: 0.8100 (mmmm) REVERT: A 274 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6150 (mp) REVERT: B 24 LYS cc_start: 0.7432 (mtpp) cc_final: 0.6878 (mmtm) REVERT: B 124 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8806 (mp) REVERT: B 165 ASP cc_start: 0.7810 (p0) cc_final: 0.7584 (p0) REVERT: B 289 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7783 (mttt) REVERT: D 3 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7593 (pttm) REVERT: D 81 ASP cc_start: 0.7699 (t70) cc_final: 0.7477 (t0) REVERT: E 126 CYS cc_start: 0.5843 (OUTLIER) cc_final: 0.4772 (m) REVERT: E 141 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8971 (mpp) REVERT: E 216 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7497 (ttmm) REVERT: E 253 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: F 35 LYS cc_start: 0.8127 (mttp) cc_final: 0.7881 (mmtp) REVERT: F 93 ASN cc_start: 0.8191 (t0) cc_final: 0.7825 (t0) REVERT: G 4 LEU cc_start: 0.5087 (OUTLIER) cc_final: 0.4886 (mm) REVERT: G 93 ASN cc_start: 0.7191 (OUTLIER) cc_final: 0.6773 (t0) REVERT: G 98 ILE cc_start: 0.6775 (mp) cc_final: 0.6560 (mp) REVERT: G 148 ASP cc_start: 0.7082 (m-30) cc_final: 0.6824 (m-30) REVERT: G 158 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7264 (mtt180) REVERT: G 165 ASP cc_start: 0.6307 (OUTLIER) cc_final: 0.5787 (t0) REVERT: G 178 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6773 (mp10) REVERT: G 186 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7867 (tm-30) REVERT: G 289 LYS cc_start: 0.7570 (ttmm) cc_final: 0.7168 (tttt) REVERT: H 35 LYS cc_start: 0.7715 (mttt) cc_final: 0.6902 (pttp) REVERT: H 60 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7524 (tt) REVERT: H 61 LYS cc_start: 0.8464 (mmmm) cc_final: 0.7988 (mppt) REVERT: H 113 LYS cc_start: 0.6502 (mttt) cc_final: 0.5909 (mttt) REVERT: H 289 LYS cc_start: 0.8285 (mttt) cc_final: 0.7589 (mmtm) outliers start: 56 outliers final: 21 residues processed: 287 average time/residue: 0.7124 time to fit residues: 225.9923 Evaluate side-chains 286 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 199 optimal weight: 6.9990 chunk 71 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN B 189 ASN D 93 ASN D 186 GLN D 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103638 restraints weight = 22397.872| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.06 r_work: 0.3123 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20140 Z= 0.135 Angle : 0.498 8.631 27516 Z= 0.257 Chirality : 0.045 0.217 3160 Planarity : 0.004 0.065 3381 Dihedral : 13.369 177.578 3316 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.10 % Allowed : 17.92 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.05 % 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: 1.31 (0.18), residues: 2334 helix: 2.32 (0.17), residues: 884 sheet: 0.77 (0.30), residues: 274 loop : -0.21 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 85 TYR 0.020 0.001 TYR C 71 PHE 0.008 0.001 PHE H 172 TRP 0.015 0.001 TRP E 5 HIS 0.003 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (20140) covalent geometry : angle 0.49780 / 0.26 (27516) hydrogen bonds : bond 0.03490 / 2.35 ( 870) hydrogen bonds : angle 4.66627 / 3.36 ( 2474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 260 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8239 (t70) cc_final: 0.7726 (t0) REVERT: A 58 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8352 (mm) REVERT: A 61 LYS cc_start: 0.8873 (tttt) cc_final: 0.8104 (mmmm) REVERT: A 274 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6169 (mp) REVERT: B 24 LYS cc_start: 0.7464 (mtpp) cc_final: 0.6900 (mmtm) REVERT: B 148 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: B 165 ASP cc_start: 0.7820 (p0) cc_final: 0.7616 (p0) REVERT: B 289 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7765 (mttt) REVERT: D 3 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7601 (pttm) REVERT: D 81 ASP cc_start: 0.7702 (t70) cc_final: 0.7477 (t0) REVERT: E 26 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: E 126 CYS cc_start: 0.6110 (OUTLIER) cc_final: 0.4948 (m) REVERT: E 141 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8983 (mpp) REVERT: E 199 ARG cc_start: 0.7918 (mmp80) cc_final: 0.7608 (mmt-90) REVERT: E 216 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7576 (ttmm) REVERT: E 253 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: F 29 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.6856 (mmm) REVERT: F 35 LYS cc_start: 0.8147 (mttp) cc_final: 0.7783 (mmtp) REVERT: F 93 ASN cc_start: 0.8197 (t0) cc_final: 0.7827 (t0) REVERT: G 4 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4904 (mm) REVERT: G 98 ILE cc_start: 0.6915 (mp) cc_final: 0.6705 (mp) REVERT: G 114 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.6240 (ptmm) REVERT: G 148 ASP cc_start: 0.7104 (m-30) cc_final: 0.6835 (m-30) REVERT: G 158 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7284 (mtt180) REVERT: G 165 ASP cc_start: 0.6296 (OUTLIER) cc_final: 0.5747 (t0) REVERT: G 178 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.6771 (mp10) REVERT: G 186 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7855 (tm-30) REVERT: G 289 LYS cc_start: 0.7549 (ttmm) cc_final: 0.7147 (tttt) REVERT: H 35 LYS cc_start: 0.7732 (mttt) cc_final: 0.6910 (pttp) REVERT: H 60 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7613 (tt) REVERT: H 61 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8031 (mppt) REVERT: H 113 LYS cc_start: 0.6592 (mttt) cc_final: 0.5999 (mttt) REVERT: H 289 LYS cc_start: 0.8305 (mttt) cc_final: 0.7616 (mmtm) outliers start: 63 outliers final: 29 residues processed: 291 average time/residue: 0.7288 time to fit residues: 234.8305 Evaluate side-chains 296 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 294 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 178 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN B 178 GLN C 66 ASN D 186 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.147733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.103198 restraints weight = 22377.770| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.16 r_work: 0.3112 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20140 Z= 0.141 Angle : 0.504 8.594 27516 Z= 0.260 Chirality : 0.045 0.234 3160 Planarity : 0.004 0.069 3381 Dihedral : 13.351 175.786 3316 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.00 % Allowed : 18.56 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.05 % 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: 1.33 (0.18), residues: 2334 helix: 2.32 (0.17), residues: 884 sheet: 0.82 (0.30), residues: 274 loop : -0.19 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 16 TYR 0.019 0.001 TYR C 71 PHE 0.008 0.001 PHE G 172 TRP 0.015 0.001 TRP E 5 HIS 0.003 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (20140) covalent geometry : angle 0.50399 / 0.26 (27516) hydrogen bonds : bond 0.03469 / 2.34 ( 870) hydrogen bonds : angle 4.64203 / 3.35 ( 2474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 258 time to evaluate : 0.807 Fit side-chains REVERT: A 22 ASP cc_start: 0.8343 (t70) cc_final: 0.7828 (t0) REVERT: A 25 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.7958 (ttm-80) REVERT: A 61 LYS cc_start: 0.8872 (tttt) cc_final: 0.8070 (mmmm) REVERT: A 274 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6124 (mp) REVERT: B 24 LYS cc_start: 0.7462 (mtpp) cc_final: 0.6883 (mmtm) REVERT: B 85 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7046 (mtm-85) REVERT: B 100 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7455 (ttt-90) REVERT: B 148 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: B 289 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7787 (mttt) REVERT: C 251 GLU cc_start: 0.8234 (tp30) cc_final: 0.7925 (tp30) REVERT: D 3 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7589 (pttm) REVERT: D 81 ASP cc_start: 0.7727 (t70) cc_final: 0.7509 (t0) REVERT: E 26 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: E 126 CYS cc_start: 0.5945 (OUTLIER) cc_final: 0.4795 (m) REVERT: E 141 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8988 (mpp) REVERT: E 199 ARG cc_start: 0.7927 (mmp80) cc_final: 0.7644 (mmt-90) REVERT: E 216 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7583 (ttmm) REVERT: E 253 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: F 93 ASN cc_start: 0.8206 (t0) cc_final: 0.7840 (t0) REVERT: G 98 ILE cc_start: 0.6917 (mp) cc_final: 0.6703 (mp) REVERT: G 114 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.6218 (ptmm) REVERT: G 148 ASP cc_start: 0.7058 (m-30) cc_final: 0.6791 (m-30) REVERT: G 158 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7249 (mtt180) REVERT: G 165 ASP cc_start: 0.6363 (OUTLIER) cc_final: 0.5797 (t0) REVERT: G 178 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.6765 (mp10) REVERT: G 186 GLN cc_start: 0.8336 (tm-30) cc_final: 0.7860 (tm-30) REVERT: G 289 LYS cc_start: 0.7564 (ttmm) cc_final: 0.7200 (tttt) REVERT: H 35 LYS cc_start: 0.7717 (mttt) cc_final: 0.6898 (pttp) REVERT: H 60 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7607 (tt) REVERT: H 61 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8033 (mppt) REVERT: H 104 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7257 (tp30) REVERT: H 113 LYS cc_start: 0.6629 (mttt) cc_final: 0.6051 (mttt) REVERT: H 289 LYS cc_start: 0.8340 (mttt) cc_final: 0.7659 (mmtm) outliers start: 61 outliers final: 31 residues processed: 289 average time/residue: 0.8102 time to fit residues: 258.0954 Evaluate side-chains 296 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 294 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 86 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 185 optimal weight: 0.0570 chunk 56 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN C 66 ASN D 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.148228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104315 restraints weight = 22435.782| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.00 r_work: 0.3125 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20140 Z= 0.123 Angle : 0.489 6.855 27516 Z= 0.253 Chirality : 0.044 0.233 3160 Planarity : 0.004 0.072 3381 Dihedral : 13.292 175.375 3316 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.95 % Allowed : 18.81 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.05 % 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: 1.39 (0.18), residues: 2334 helix: 2.38 (0.17), residues: 884 sheet: 0.86 (0.30), residues: 274 loop : -0.18 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 100 TYR 0.018 0.001 TYR C 71 PHE 0.007 0.001 PHE H 172 TRP 0.016 0.001 TRP E 5 HIS 0.002 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (20140) covalent geometry : angle 0.48854 / 0.25 (27516) hydrogen bonds : bond 0.03291 / 2.22 ( 870) hydrogen bonds : angle 4.58318 / 3.30 ( 2474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 0.780 Fit side-chains REVERT: A 22 ASP cc_start: 0.8290 (t70) cc_final: 0.7890 (t0) REVERT: A 25 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.7816 (ttm170) REVERT: A 58 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8067 (mm) REVERT: A 61 LYS cc_start: 0.8881 (tttt) cc_final: 0.8089 (mmmm) REVERT: A 274 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6129 (mp) REVERT: B 24 LYS cc_start: 0.7466 (mtpp) cc_final: 0.6878 (mmtm) REVERT: B 100 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7436 (ttt-90) REVERT: B 289 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7754 (mttt) REVERT: C 251 GLU cc_start: 0.8227 (tp30) cc_final: 0.7913 (tp30) REVERT: D 3 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7596 (pttm) REVERT: D 81 ASP cc_start: 0.7710 (t70) cc_final: 0.7495 (t0) REVERT: E 26 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: E 126 CYS cc_start: 0.5903 (OUTLIER) cc_final: 0.4810 (m) REVERT: E 141 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8984 (mpp) REVERT: E 199 ARG cc_start: 0.7919 (mmp80) cc_final: 0.7646 (mmt-90) REVERT: E 216 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7500 (ttmm) REVERT: E 253 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: F 93 ASN cc_start: 0.8172 (t0) cc_final: 0.7787 (t0) REVERT: G 98 ILE cc_start: 0.6894 (mp) cc_final: 0.6678 (mp) REVERT: G 114 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.6228 (ptmm) REVERT: G 148 ASP cc_start: 0.7070 (m-30) cc_final: 0.6788 (m-30) REVERT: G 158 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7261 (mtt180) REVERT: G 165 ASP cc_start: 0.6328 (OUTLIER) cc_final: 0.5739 (t0) REVERT: G 178 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: G 186 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7871 (tm-30) REVERT: H 35 LYS cc_start: 0.7776 (mttt) cc_final: 0.6943 (pttp) REVERT: H 60 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7595 (tt) REVERT: H 61 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8030 (mppt) REVERT: H 104 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7245 (tp30) REVERT: H 113 LYS cc_start: 0.6729 (mttt) cc_final: 0.6173 (mttt) REVERT: H 183 GLN cc_start: 0.8251 (mt0) cc_final: 0.7942 (mt0) REVERT: H 289 LYS cc_start: 0.8309 (mttt) cc_final: 0.7653 (mmtm) outliers start: 60 outliers final: 29 residues processed: 290 average time/residue: 0.7858 time to fit residues: 250.5744 Evaluate side-chains 294 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 294 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 204 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN C 66 ASN D 186 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107928 restraints weight = 24262.285| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.87 r_work: 0.3321 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20140 Z= 0.116 Angle : 0.489 9.812 27516 Z= 0.251 Chirality : 0.044 0.231 3160 Planarity : 0.004 0.074 3381 Dihedral : 13.246 175.644 3316 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.90 % Allowed : 19.05 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.05 % 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: 1.44 (0.18), residues: 2334 helix: 2.43 (0.17), residues: 884 sheet: 0.88 (0.31), residues: 274 loop : -0.16 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 85 TYR 0.017 0.001 TYR C 71 PHE 0.007 0.001 PHE G 172 TRP 0.017 0.001 TRP E 5 HIS 0.002 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (20140) covalent geometry : angle 0.48878 / 0.25 (27516) hydrogen bonds : bond 0.03202 / 2.17 ( 870) hydrogen bonds : angle 4.54613 / 3.27 ( 2474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 259 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8239 (t70) cc_final: 0.7931 (t0) REVERT: A 58 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8481 (mm) REVERT: A 61 LYS cc_start: 0.8883 (tttt) cc_final: 0.8171 (mmmm) REVERT: A 274 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6330 (mp) REVERT: B 24 LYS cc_start: 0.7601 (mtpp) cc_final: 0.7019 (mmtm) REVERT: B 100 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7470 (ttt-90) REVERT: B 103 ILE cc_start: 0.8117 (mm) cc_final: 0.7892 (mp) REVERT: B 148 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: B 289 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7839 (mttt) REVERT: C 251 GLU cc_start: 0.8268 (tp30) cc_final: 0.7954 (tp30) REVERT: D 3 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7635 (pttm) REVERT: E 3 LYS cc_start: 0.8470 (mmmm) cc_final: 0.8206 (mmpt) REVERT: E 6 ARG cc_start: 0.8325 (ttm170) cc_final: 0.8115 (ttm170) REVERT: E 126 CYS cc_start: 0.5896 (OUTLIER) cc_final: 0.4871 (m) REVERT: E 141 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.9003 (mpp) REVERT: E 199 ARG cc_start: 0.7996 (mmp80) cc_final: 0.7732 (mmt-90) REVERT: E 216 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7701 (ttmm) REVERT: E 253 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: F 80 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6660 (mp) REVERT: F 93 ASN cc_start: 0.8246 (t0) cc_final: 0.7891 (t0) REVERT: G 98 ILE cc_start: 0.6963 (mp) cc_final: 0.6741 (mp) REVERT: G 114 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.6159 (ptmm) REVERT: G 148 ASP cc_start: 0.7357 (m-30) cc_final: 0.7066 (m-30) REVERT: G 158 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7402 (mtt180) REVERT: G 165 ASP cc_start: 0.6410 (OUTLIER) cc_final: 0.5803 (t0) REVERT: G 178 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: G 186 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7883 (tm-30) REVERT: G 289 LYS cc_start: 0.7741 (ttmm) cc_final: 0.7280 (tttt) REVERT: H 35 LYS cc_start: 0.7955 (mttt) cc_final: 0.7087 (pttp) REVERT: H 60 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7821 (tt) REVERT: H 61 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8117 (mppt) REVERT: H 66 ASN cc_start: 0.7467 (m-40) cc_final: 0.6981 (t0) REVERT: H 104 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7260 (tp30) REVERT: H 113 LYS cc_start: 0.6944 (mttt) cc_final: 0.6330 (mttt) REVERT: H 183 GLN cc_start: 0.8404 (mt0) cc_final: 0.8130 (mt0) REVERT: H 289 LYS cc_start: 0.8416 (mttt) cc_final: 0.7822 (mmtm) outliers start: 59 outliers final: 29 residues processed: 292 average time/residue: 0.7511 time to fit residues: 241.8608 Evaluate side-chains 299 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 294 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 200 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 175 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN C 66 ASN D 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.151281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107347 restraints weight = 24053.155| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.86 r_work: 0.3311 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20140 Z= 0.134 Angle : 0.503 8.960 27516 Z= 0.258 Chirality : 0.045 0.240 3160 Planarity : 0.004 0.078 3381 Dihedral : 13.236 175.257 3316 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.71 % Allowed : 19.30 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.05 % 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: 1.42 (0.18), residues: 2334 helix: 2.39 (0.17), residues: 884 sheet: 0.91 (0.30), residues: 274 loop : -0.16 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 16 TYR 0.019 0.001 TYR C 71 PHE 0.008 0.001 PHE H 172 TRP 0.018 0.001 TRP E 5 HIS 0.003 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (20140) covalent geometry : angle 0.50298 / 0.26 (27516) hydrogen bonds : bond 0.03325 / 2.25 ( 870) hydrogen bonds : angle 4.56899 / 3.29 ( 2474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 256 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8272 (t70) cc_final: 0.7951 (t0) REVERT: A 61 LYS cc_start: 0.8893 (tttt) cc_final: 0.8175 (mmmm) REVERT: A 274 ILE cc_start: 0.6912 (OUTLIER) cc_final: 0.6301 (mp) REVERT: B 24 LYS cc_start: 0.7583 (mtpp) cc_final: 0.7010 (mmtm) REVERT: B 100 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7484 (ttt-90) REVERT: B 148 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: B 289 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7830 (mttt) REVERT: C 251 GLU cc_start: 0.8295 (tp30) cc_final: 0.8001 (tp30) REVERT: D 3 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7643 (pttm) REVERT: D 132 ARG cc_start: 0.8991 (ttp80) cc_final: 0.8682 (ttt180) REVERT: E 3 LYS cc_start: 0.8462 (mmmm) cc_final: 0.8181 (mmpt) REVERT: E 126 CYS cc_start: 0.5897 (OUTLIER) cc_final: 0.4798 (m) REVERT: E 141 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.9005 (mpp) REVERT: E 199 ARG cc_start: 0.7978 (mmp80) cc_final: 0.7723 (mmt-90) REVERT: E 216 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7715 (ttmm) REVERT: E 253 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: F 29 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.6870 (mmm) REVERT: F 80 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6635 (mp) REVERT: F 93 ASN cc_start: 0.8221 (t0) cc_final: 0.7865 (t0) REVERT: G 98 ILE cc_start: 0.6932 (mp) cc_final: 0.6711 (mp) REVERT: G 114 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6169 (ptmm) REVERT: G 148 ASP cc_start: 0.7377 (m-30) cc_final: 0.7096 (m-30) REVERT: G 158 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7380 (mtt180) REVERT: G 165 ASP cc_start: 0.6380 (OUTLIER) cc_final: 0.5745 (t0) REVERT: G 178 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6909 (mp10) REVERT: G 186 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7877 (tm-30) REVERT: G 289 LYS cc_start: 0.7708 (ttmm) cc_final: 0.7245 (tttt) REVERT: H 35 LYS cc_start: 0.7929 (mttt) cc_final: 0.7062 (pttp) REVERT: H 60 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7795 (tt) REVERT: H 61 LYS cc_start: 0.8516 (mmmm) cc_final: 0.8102 (mppt) REVERT: H 66 ASN cc_start: 0.7421 (m-40) cc_final: 0.6976 (t0) REVERT: H 104 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7275 (tp30) REVERT: H 113 LYS cc_start: 0.6904 (mttt) cc_final: 0.6287 (mttt) REVERT: H 183 GLN cc_start: 0.8395 (mt0) cc_final: 0.8085 (mt0) REVERT: H 289 LYS cc_start: 0.8416 (mttt) cc_final: 0.7816 (mmtm) outliers start: 55 outliers final: 33 residues processed: 289 average time/residue: 0.7211 time to fit residues: 229.0848 Evaluate side-chains 300 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 168 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN C 66 ASN D 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.151876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108091 restraints weight = 24242.940| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.87 r_work: 0.3322 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20140 Z= 0.113 Angle : 0.484 6.741 27516 Z= 0.250 Chirality : 0.044 0.232 3160 Planarity : 0.004 0.080 3381 Dihedral : 13.195 175.739 3316 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.46 % Allowed : 19.50 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.05 % 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: 1.49 (0.18), residues: 2334 helix: 2.45 (0.17), residues: 890 sheet: 0.96 (0.31), residues: 274 loop : -0.14 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 100 TYR 0.017 0.001 TYR C 71 PHE 0.007 0.001 PHE H 172 TRP 0.020 0.001 TRP E 5 HIS 0.002 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (20140) covalent geometry : angle 0.48379 / 0.25 (27516) hydrogen bonds : bond 0.03140 / 2.13 ( 870) hydrogen bonds : angle 4.52920 / 3.26 ( 2474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8183 (t70) cc_final: 0.7889 (t0) REVERT: A 61 LYS cc_start: 0.8886 (tttt) cc_final: 0.8181 (mmmm) REVERT: A 274 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6328 (mp) REVERT: B 24 LYS cc_start: 0.7594 (mtpp) cc_final: 0.7062 (mmtm) REVERT: B 100 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7455 (ttt-90) REVERT: B 148 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: B 186 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8172 (tm-30) REVERT: C 251 GLU cc_start: 0.8267 (tp30) cc_final: 0.7955 (tp30) REVERT: D 3 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7657 (pttm) REVERT: D 132 ARG cc_start: 0.8991 (ttp80) cc_final: 0.8678 (ttt180) REVERT: E 126 CYS cc_start: 0.5863 (OUTLIER) cc_final: 0.4826 (m) REVERT: E 141 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8986 (mpp) REVERT: E 199 ARG cc_start: 0.7980 (mmp80) cc_final: 0.7725 (mmt-90) REVERT: E 253 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: F 80 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6685 (mp) REVERT: F 93 ASN cc_start: 0.8229 (t0) cc_final: 0.7883 (t0) REVERT: G 98 ILE cc_start: 0.6936 (mp) cc_final: 0.6716 (mp) REVERT: G 114 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.6153 (ptmm) REVERT: G 148 ASP cc_start: 0.7455 (m-30) cc_final: 0.7201 (m-30) REVERT: G 158 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7369 (mtt180) REVERT: G 165 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.5667 (t0) REVERT: G 178 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6921 (mp10) REVERT: G 186 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7884 (tm-30) REVERT: G 265 MET cc_start: 0.8625 (mmt) cc_final: 0.8010 (mmt) REVERT: G 289 LYS cc_start: 0.7717 (ttmm) cc_final: 0.7196 (tmtm) REVERT: H 35 LYS cc_start: 0.7954 (mttt) cc_final: 0.7083 (pttp) REVERT: H 60 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7839 (tt) REVERT: H 61 LYS cc_start: 0.8510 (mmmm) cc_final: 0.8111 (mppt) REVERT: H 66 ASN cc_start: 0.7379 (m-40) cc_final: 0.6938 (t0) REVERT: H 104 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7273 (tp30) REVERT: H 113 LYS cc_start: 0.6914 (mttt) cc_final: 0.6312 (mttt) REVERT: H 158 ARG cc_start: 0.7786 (mtp180) cc_final: 0.7502 (mtp85) REVERT: H 183 GLN cc_start: 0.8443 (mt0) cc_final: 0.8147 (mt0) REVERT: H 289 LYS cc_start: 0.8406 (mttt) cc_final: 0.7812 (mmtm) outliers start: 50 outliers final: 31 residues processed: 285 average time/residue: 0.7584 time to fit residues: 237.4675 Evaluate side-chains 298 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 232 optimal weight: 20.0000 chunk 23 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 178 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 0.0470 chunk 46 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN C 66 ASN D 186 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.148948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106370 restraints weight = 22724.768| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.95 r_work: 0.3115 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20140 Z= 0.106 Angle : 0.482 9.646 27516 Z= 0.248 Chirality : 0.044 0.225 3160 Planarity : 0.004 0.087 3381 Dihedral : 13.146 176.567 3316 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.26 % Allowed : 19.79 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.05 % 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: 1.49 (0.18), residues: 2334 helix: 2.45 (0.17), residues: 894 sheet: 0.83 (0.31), residues: 265 loop : -0.11 (0.19), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG B 85 TYR 0.017 0.001 TYR C 71 PHE 0.007 0.001 PHE G 172 TRP 0.020 0.001 TRP E 5 HIS 0.002 0.001 HIS E 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (20140) covalent geometry : angle 0.48169 / 0.25 (27516) hydrogen bonds : bond 0.03034 / 2.05 ( 870) hydrogen bonds : angle 4.49537 / 3.23 ( 2474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7680.61 seconds wall clock time: 131 minutes 5.54 seconds (7865.54 seconds total)