Starting phenix.real_space_refine on Sat Jul 4 16:26:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wwv_32874/07_2026/7wwv_32874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwv_32874/07_2026/7wwv_32874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wwv_32874/07_2026/7wwv_32874.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wwv_32874/07_2026/7wwv_32874.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wwv_32874/07_2026/7wwv_32874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwv_32874/07_2026/7wwv_32874.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwv_32874/07_2026/7wwv_32874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwv_32874/07_2026/7wwv_32874.cif" } resolution = 3.2 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3121 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 117 5.49 5 S 67 5.16 5 C 11978 2.51 5 N 3358 2.21 5 O 4102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19622 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1431 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain: "B" Number of atoms: 1924 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1919 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 237} Conformer: "B" Number of residues, atoms: 248, 1919 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 237} bond proxies already assigned to first conformer: 1950 Chain: "C" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 811 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 15, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 22, 'rna3p': 16} Chain: "O" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 952 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "N" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 662 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Time building chain proxies: 4.57, per 1000 atoms: 0.23 Number of scatterers: 19622 At special positions: 0 Unit cell: (176.64, 151.8, 111.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 117 15.00 O 4102 8.00 N 3358 7.00 C 11978 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: 1.71 Conformation dependent library (CDL) restraints added in 835.8 milliseconds 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 37 sheets defined 26.7% alpha, 22.5% beta 39 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.773A pdb=" N LYS A 12 " --> pdb=" O ASP A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.886A pdb=" N ALA A 52 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.580A pdb=" N ARG A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 91 removed outlier: 4.091A pdb=" N TYR A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.715A pdb=" N ILE A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.925A pdb=" N ASN A 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS A 152 " --> pdb=" O PRO A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 152' Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.727A pdb=" N ASN A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.878A pdb=" N PHE B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 removed outlier: 3.530A pdb=" N ASP B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.544A pdb=" N VAL B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 removed outlier: 3.721A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 112 through 125 removed outlier: 3.562A pdb=" N ILE C 123 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 134 removed outlier: 3.520A pdb=" N VAL C 134 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 178 removed outlier: 4.659A pdb=" N MET C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.722A pdb=" N ALA C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 233 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG C 234 " --> pdb=" O GLY C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.662A pdb=" N VAL C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 297 removed outlier: 3.614A pdb=" N ALA C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 111 through 125 removed outlier: 4.507A pdb=" N LEU D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 123 " --> pdb=" O TYR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 134 Processing helix chain 'D' and resid 164 through 178 removed outlier: 3.574A pdb=" N GLU D 168 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 3.506A pdb=" N ILE D 233 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 279 removed outlier: 3.611A pdb=" N VAL D 278 " --> pdb=" O MET D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 297 Processing helix chain 'E' and resid 98 through 107 Processing helix chain 'E' and resid 111 through 125 removed outlier: 4.014A pdb=" N LEU E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE E 123 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 134 Processing helix chain 'E' and resid 163 through 178 removed outlier: 4.028A pdb=" N ALA E 167 " --> pdb=" O ASP E 163 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU E 168 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE E 169 " --> pdb=" O ASP E 165 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 removed outlier: 3.603A pdb=" N ALA E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE E 233 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG E 234 " --> pdb=" O GLY E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 284 through 297 Processing helix chain 'F' and resid 98 through 107 Processing helix chain 'F' and resid 111 through 125 removed outlier: 4.505A pdb=" N LEU F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 134 Processing helix chain 'F' and resid 163 through 178 removed outlier: 3.849A pdb=" N ALA F 167 " --> pdb=" O ASP F 163 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU F 168 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 234 removed outlier: 3.585A pdb=" N ALA F 232 " --> pdb=" O LYS F 228 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 233 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 234 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 278 removed outlier: 3.520A pdb=" N LEU F 273 " --> pdb=" O ASP F 269 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL F 278 " --> pdb=" O MET F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 Processing helix chain 'G' and resid 98 through 107 Processing helix chain 'G' and resid 111 through 125 removed outlier: 4.425A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 134 Processing helix chain 'G' and resid 164 through 178 removed outlier: 3.990A pdb=" N GLU G 168 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE G 169 " --> pdb=" O ASP G 165 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 234 removed outlier: 3.612A pdb=" N ALA G 232 " --> pdb=" O LYS G 228 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 233 " --> pdb=" O ILE G 229 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG G 234 " --> pdb=" O GLY G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 279 removed outlier: 3.706A pdb=" N VAL G 278 " --> pdb=" O MET G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 297 Processing helix chain 'H' and resid 98 through 107 Processing helix chain 'H' and resid 111 through 125 removed outlier: 4.309A pdb=" N LEU H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE H 123 " --> pdb=" O TYR H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 134 Processing helix chain 'H' and resid 166 through 178 removed outlier: 4.319A pdb=" N MET H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 234 removed outlier: 3.627A pdb=" N ALA H 232 " --> pdb=" O LYS H 228 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE H 233 " --> pdb=" O ILE H 229 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG H 234 " --> pdb=" O GLY H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 279 removed outlier: 3.612A pdb=" N VAL H 278 " --> pdb=" O MET H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 297 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 3.502A pdb=" N ILE A 32 " --> pdb=" O HIS A 19 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS A 19 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 107 removed outlier: 8.823A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 159 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 161 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR B 52 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N ASP B 163 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 15.511A pdb=" N VAL B 50 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 97 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE B 57 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP B 95 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL B 59 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU B 93 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA B 94 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP B 13 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLY B 96 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYS B 11 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE B 98 " --> pdb=" O ASN B 9 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 3 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.722A pdb=" N ILE B 126 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS B 11 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 3 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE B 98 " --> pdb=" O ASN B 9 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYS B 11 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLY B 96 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP B 13 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA B 94 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU B 93 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL B 59 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP B 95 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE B 57 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 97 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 15.511A pdb=" N VAL B 50 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N ASP B 163 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR B 52 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 161 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 159 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA B 205 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LYS B 191 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 207 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 185 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR B 213 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL B 183 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE B 215 " --> pdb=" O PRO B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 142 removed outlier: 3.793A pdb=" N GLN A 165 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 16 through 18 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 18 removed outlier: 3.609A pdb=" N LEU C 77 " --> pdb=" O MET C 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 42 through 47 Processing sheet with id=AB2, first strand: chain 'C' and resid 217 through 218 Processing sheet with id=AB3, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.700A pdb=" N VAL C 260 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.568A pdb=" N GLY D 299 " --> pdb=" O TYR D 12 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 25 current: chain 'D' and resid 140 through 145 Processing sheet with id=AB6, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.651A pdb=" N THR D 35 " --> pdb=" O ALA D 25 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 77 through 86 current: chain 'D' and resid 217 through 218 Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 47 Processing sheet with id=AB8, first strand: chain 'D' and resid 254 through 255 removed outlier: 3.543A pdb=" N VAL D 260 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.702A pdb=" N GLY E 299 " --> pdb=" O TYR E 12 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 21 through 26 current: chain 'E' and resid 140 through 145 Processing sheet with id=AC2, first strand: chain 'E' and resid 35 through 36 removed outlier: 3.611A pdb=" N THR E 35 " --> pdb=" O ALA E 25 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 76 through 86 current: chain 'E' and resid 217 through 218 Processing sheet with id=AC3, first strand: chain 'E' and resid 42 through 46 Processing sheet with id=AC4, first strand: chain 'E' and resid 254 through 255 removed outlier: 3.661A pdb=" N VAL E 260 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.766A pdb=" N GLY F 299 " --> pdb=" O TYR F 12 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AC7, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AC8, first strand: chain 'F' and resid 41 through 47 Processing sheet with id=AC9, first strand: chain 'F' and resid 217 through 218 Processing sheet with id=AD1, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.513A pdb=" N GLY G 299 " --> pdb=" O TYR G 12 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 21 through 26 current: chain 'G' and resid 140 through 145 Processing sheet with id=AD3, first strand: chain 'G' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 76 through 86 current: chain 'G' and resid 217 through 218 Processing sheet with id=AD4, first strand: chain 'G' and resid 41 through 46 Processing sheet with id=AD5, first strand: chain 'G' and resid 254 through 255 removed outlier: 3.554A pdb=" N VAL G 260 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AD7, first strand: chain 'H' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 21 through 26 current: chain 'H' and resid 140 through 144 Processing sheet with id=AD8, first strand: chain 'H' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 76 through 86 current: chain 'H' and resid 217 through 218 Processing sheet with id=AD9, first strand: chain 'H' and resid 41 through 47 Processing sheet with id=AE1, first strand: chain 'H' and resid 254 through 255 removed outlier: 3.509A pdb=" N VAL H 260 " --> pdb=" O VAL H 255 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5934 1.34 - 1.46: 4151 1.46 - 1.58: 9787 1.58 - 1.70: 231 1.70 - 1.82: 123 Bond restraints: 20226 Sorted by residual: bond pdb=" C3' DT O 8 " pdb=" C2' DT O 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.77e+00 bond pdb=" C3' DA N 28 " pdb=" C2' DA N 28 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.48e+00 bond pdb=" N9 DA O 14 " pdb=" C4 DA O 14 " ideal model delta sigma weight residual 1.374 1.391 -0.017 6.00e-03 2.78e+04 7.98e+00 bond pdb=" C3' DT N 15 " pdb=" C2' DT N 15 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.82e+00 bond pdb=" C3' DA N 19 " pdb=" C2' DA N 19 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.19e+00 ... (remaining 20221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 27398 1.88 - 3.76: 518 3.76 - 5.64: 20 5.64 - 7.52: 7 7.52 - 9.39: 3 Bond angle restraints: 27946 Sorted by residual: angle pdb=" O4' DA O 14 " pdb=" C4' DA O 14 " pdb=" C3' DA O 14 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.49e+01 angle pdb=" C LEU D 107 " pdb=" N GLU D 108 " pdb=" CA GLU D 108 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C LEU C 107 " pdb=" N GLU C 108 " pdb=" CA GLU C 108 " ideal model delta sigma weight residual 122.61 130.17 -7.56 1.56e+00 4.11e-01 2.35e+01 angle pdb=" C LEU F 107 " pdb=" N GLU F 108 " pdb=" CA GLU F 108 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 angle pdb=" N3 DT N 15 " pdb=" C4 DT N 15 " pdb=" O4 DT N 15 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 27941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 11289 35.63 - 71.26: 367 71.26 - 106.88: 30 106.88 - 142.51: 1 142.51 - 178.14: 2 Dihedral angle restraints: 11689 sinusoidal: 5309 harmonic: 6380 Sorted by residual: dihedral pdb=" O4' U M 32 " pdb=" C1' U M 32 " pdb=" N1 U M 32 " pdb=" C2 U M 32 " ideal model delta sinusoidal sigma weight residual -128.00 50.14 -178.14 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 3 " pdb=" C1' U M 3 " pdb=" N1 U M 3 " pdb=" C2 U M 3 " ideal model delta sinusoidal sigma weight residual -128.00 48.57 -176.57 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 35 " pdb=" C1' U M 35 " pdb=" N1 U M 35 " pdb=" C2 U M 35 " ideal model delta sinusoidal sigma weight residual -160.00 -99.63 -60.37 1 1.50e+01 4.44e-03 2.16e+01 ... (remaining 11686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2316 0.039 - 0.077: 664 0.077 - 0.116: 180 0.116 - 0.155: 33 0.155 - 0.193: 4 Chirality restraints: 3197 Sorted by residual: chirality pdb=" CB THR F 268 " pdb=" CA THR F 268 " pdb=" OG1 THR F 268 " pdb=" CG2 THR F 268 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CB THR D 268 " pdb=" CA THR D 268 " pdb=" OG1 THR D 268 " pdb=" CG2 THR D 268 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CB THR G 268 " pdb=" CA THR G 268 " pdb=" OG1 THR G 268 " pdb=" CG2 THR G 268 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.00e-01 ... (remaining 3194 not shown) Planarity restraints: 3231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 239 " -0.015 2.00e-02 2.50e+03 1.27e-02 4.02e+00 pdb=" CG TRP C 239 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 239 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 239 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 239 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 239 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 239 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 239 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 239 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 156 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 157 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 159 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C GLU G 159 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU G 159 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE G 160 " 0.009 2.00e-02 2.50e+03 ... (remaining 3228 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1452 2.74 - 3.28: 18514 3.28 - 3.82: 30570 3.82 - 4.36: 36717 4.36 - 4.90: 63982 Nonbonded interactions: 151235 Sorted by model distance: nonbonded pdb=" O ALA H 45 " pdb=" O2' A M 13 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASP F 226 " pdb=" NE2 GLN F 227 " model vdw 2.242 3.120 nonbonded pdb=" OH TYR H 117 " pdb=" O ASP H 161 " model vdw 2.243 3.040 nonbonded pdb=" O ALA D 45 " pdb=" O2' A M 37 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR F 117 " pdb=" O ASP F 161 " model vdw 2.246 3.040 ... (remaining 151230 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.680 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20226 Z= 0.232 Angle : 0.602 9.395 27946 Z= 0.422 Chirality : 0.040 0.193 3197 Planarity : 0.003 0.042 3231 Dihedral : 16.137 178.140 7615 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.43 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.19), residues: 2218 helix: 1.34 (0.25), residues: 485 sheet: 1.37 (0.30), residues: 384 loop : -1.78 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 133 TYR 0.019 0.001 TYR D 240 PHE 0.021 0.001 PHE E 90 TRP 0.034 0.001 TRP C 239 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.23 (20226) covalent geometry : angle 0.60205 / 0.42 (27946) hydrogen bonds : bond 0.17787 / 11.56 ( 620) hydrogen bonds : angle 6.54922 / 4.39 ( 1750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 115 LEU cc_start: 0.7232 (mt) cc_final: 0.6989 (mt) REVERT: B 235 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7250 (tp30) REVERT: B 236 ASN cc_start: 0.6617 (t0) cc_final: 0.6350 (t0) REVERT: D 191 MET cc_start: 0.7019 (mpp) cc_final: 0.6778 (mmm) REVERT: F 91 LYS cc_start: 0.7728 (tttp) cc_final: 0.7451 (tmtt) REVERT: G 182 PHE cc_start: 0.7848 (p90) cc_final: 0.7641 (p90) REVERT: G 188 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6975 (mt-10) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1298 time to fit residues: 63.7158 Evaluate side-chains 234 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.0980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN C 63 GLN C 279 ASN E 214 GLN F 203 GLN F 214 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.173106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.133304 restraints weight = 29528.342| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.48 r_work: 0.3274 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20226 Z= 0.145 Angle : 0.568 7.940 27946 Z= 0.322 Chirality : 0.043 0.244 3197 Planarity : 0.003 0.040 3231 Dihedral : 16.595 177.946 3725 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.75 % Favored : 91.16 % Rotamer: Outliers : 0.98 % Allowed : 7.01 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.19), residues: 2218 helix: 1.29 (0.23), residues: 498 sheet: 1.43 (0.31), residues: 372 loop : -1.74 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 263 TYR 0.015 0.001 TYR D 240 PHE 0.015 0.001 PHE B 202 TRP 0.015 0.001 TRP C 239 HIS 0.002 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (20226) covalent geometry : angle 0.56824 / 0.32 (27946) hydrogen bonds : bond 0.05264 / 3.52 ( 620) hydrogen bonds : angle 4.31428 / 2.84 ( 1750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 174 GLU cc_start: 0.7526 (pp20) cc_final: 0.6692 (tm-30) REVERT: B 48 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7439 (mptt) REVERT: B 236 ASN cc_start: 0.7039 (t0) cc_final: 0.6520 (t0) REVERT: G 188 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7792 (mt-10) REVERT: H 207 GLU cc_start: 0.6635 (tp30) cc_final: 0.6421 (tp30) outliers start: 18 outliers final: 11 residues processed: 264 average time/residue: 0.1295 time to fit residues: 55.0511 Evaluate side-chains 236 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 225 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 90 optimal weight: 0.0470 chunk 148 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 120 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 194 optimal weight: 0.0050 chunk 150 optimal weight: 0.5980 chunk 195 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.4694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 ASN E 214 GLN H 20 ASN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.175881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135970 restraints weight = 34258.865| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.21 r_work: 0.3240 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20226 Z= 0.115 Angle : 0.531 8.042 27946 Z= 0.303 Chirality : 0.041 0.296 3197 Planarity : 0.003 0.039 3231 Dihedral : 16.690 178.168 3725 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.30 % Favored : 91.52 % Rotamer: Outliers : 1.20 % Allowed : 9.30 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.19), residues: 2218 helix: 1.40 (0.23), residues: 493 sheet: 1.44 (0.30), residues: 372 loop : -1.68 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 263 TYR 0.026 0.001 TYR A 86 PHE 0.016 0.001 PHE B 202 TRP 0.015 0.001 TRP F 130 HIS 0.002 0.001 HIS F 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.12 (20226) covalent geometry : angle 0.53101 / 0.30 (27946) hydrogen bonds : bond 0.04402 / 2.98 ( 620) hydrogen bonds : angle 4.04361 / 2.65 ( 1750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: B 48 LYS cc_start: 0.7734 (mmmt) cc_final: 0.6857 (mtpp) REVERT: B 236 ASN cc_start: 0.7032 (t0) cc_final: 0.6506 (t0) REVERT: D 38 MET cc_start: 0.7936 (mmp) cc_final: 0.7729 (mmp) REVERT: D 210 LYS cc_start: 0.8200 (mttp) cc_final: 0.7957 (mmmt) REVERT: G 188 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7940 (mt-10) REVERT: G 211 LEU cc_start: 0.9072 (mp) cc_final: 0.8730 (mt) REVERT: H 207 GLU cc_start: 0.6774 (tp30) cc_final: 0.6542 (tp30) outliers start: 22 outliers final: 16 residues processed: 264 average time/residue: 0.1339 time to fit residues: 56.4218 Evaluate side-chains 242 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 255 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 170 optimal weight: 8.9990 chunk 178 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN B 74 GLN D 17 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.172178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130038 restraints weight = 35814.597| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.22 r_work: 0.3140 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20226 Z= 0.152 Angle : 0.562 6.742 27946 Z= 0.319 Chirality : 0.042 0.200 3197 Planarity : 0.003 0.037 3231 Dihedral : 16.749 177.872 3725 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.29 % Favored : 90.53 % Rotamer: Outliers : 2.28 % Allowed : 10.11 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 2218 helix: 1.26 (0.23), residues: 499 sheet: 1.32 (0.30), residues: 372 loop : -1.73 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 14 TYR 0.018 0.001 TYR A 86 PHE 0.019 0.002 PHE H 205 TRP 0.012 0.001 TRP F 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (20226) covalent geometry : angle 0.56156 / 0.32 (27946) hydrogen bonds : bond 0.04494 / 3.03 ( 620) hydrogen bonds : angle 3.99879 / 2.64 ( 1750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: B 115 ASP cc_start: 0.8107 (t0) cc_final: 0.7903 (t0) REVERT: B 236 ASN cc_start: 0.7254 (t0) cc_final: 0.6773 (t0) REVERT: C 289 MET cc_start: 0.6089 (mmp) cc_final: 0.5609 (mtt) REVERT: D 38 MET cc_start: 0.7960 (mmp) cc_final: 0.7741 (mmp) REVERT: E 252 TYR cc_start: 0.7505 (m-80) cc_final: 0.7057 (m-10) REVERT: E 269 ASP cc_start: 0.7299 (m-30) cc_final: 0.6945 (m-30) REVERT: G 188 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8120 (mt-10) REVERT: H 275 ASP cc_start: 0.7635 (m-30) cc_final: 0.7427 (m-30) outliers start: 42 outliers final: 28 residues processed: 261 average time/residue: 0.1286 time to fit residues: 53.9361 Evaluate side-chains 250 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 92 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 230 optimal weight: 30.0000 chunk 85 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 196 optimal weight: 0.6980 chunk 111 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN C 146 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN F 20 ASN F 203 GLN F 294 ASN H 227 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.171200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129727 restraints weight = 27946.703| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.59 r_work: 0.3164 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20226 Z= 0.151 Angle : 0.556 6.787 27946 Z= 0.317 Chirality : 0.042 0.187 3197 Planarity : 0.003 0.038 3231 Dihedral : 16.772 178.380 3725 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.52 % Favored : 90.30 % Rotamer: Outliers : 2.34 % Allowed : 10.98 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.18), residues: 2218 helix: 1.25 (0.23), residues: 501 sheet: 1.05 (0.29), residues: 384 loop : -1.72 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 14 TYR 0.019 0.001 TYR A 86 PHE 0.021 0.001 PHE H 205 TRP 0.012 0.001 TRP F 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (20226) covalent geometry : angle 0.55639 / 0.32 (27946) hydrogen bonds : bond 0.04385 / 2.95 ( 620) hydrogen bonds : angle 3.96487 / 2.62 ( 1750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: A 10 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7893 (pt) REVERT: B 37 GLU cc_start: 0.7582 (tp30) cc_final: 0.7372 (tp30) REVERT: B 115 ASP cc_start: 0.8086 (t0) cc_final: 0.7883 (t0) REVERT: B 151 VAL cc_start: 0.6957 (p) cc_final: 0.6699 (p) REVERT: B 236 ASN cc_start: 0.7285 (t0) cc_final: 0.6869 (t0) REVERT: C 32 ASP cc_start: 0.7787 (m-30) cc_final: 0.7425 (p0) REVERT: D 38 MET cc_start: 0.7861 (mmp) cc_final: 0.7632 (mmp) REVERT: D 210 LYS cc_start: 0.8229 (mttp) cc_final: 0.7949 (mmmt) REVERT: G 188 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7867 (mt-10) REVERT: H 205 PHE cc_start: 0.6889 (t80) cc_final: 0.6408 (t80) outliers start: 43 outliers final: 32 residues processed: 259 average time/residue: 0.1249 time to fit residues: 52.0392 Evaluate side-chains 261 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 289 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 4 optimal weight: 0.7980 chunk 227 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 230 optimal weight: 30.0000 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 146 ASN C 279 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN H 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.172173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.131075 restraints weight = 27945.143| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.53 r_work: 0.3191 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20226 Z= 0.120 Angle : 0.532 7.291 27946 Z= 0.304 Chirality : 0.041 0.186 3197 Planarity : 0.003 0.038 3231 Dihedral : 16.762 178.939 3725 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.34 % Favored : 90.48 % Rotamer: Outliers : 2.12 % Allowed : 12.29 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.18), residues: 2218 helix: 1.32 (0.23), residues: 501 sheet: 0.97 (0.29), residues: 396 loop : -1.67 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 263 TYR 0.021 0.001 TYR A 86 PHE 0.020 0.001 PHE B 202 TRP 0.015 0.001 TRP F 130 HIS 0.002 0.001 HIS F 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (20226) covalent geometry : angle 0.53179 / 0.30 (27946) hydrogen bonds : bond 0.04100 / 2.76 ( 620) hydrogen bonds : angle 3.86347 / 2.55 ( 1750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: A 10 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.7898 (pt) REVERT: B 26 MET cc_start: 0.7912 (mmm) cc_final: 0.7616 (tpt) REVERT: B 115 ASP cc_start: 0.8096 (t0) cc_final: 0.7888 (t0) REVERT: B 151 VAL cc_start: 0.6940 (p) cc_final: 0.6714 (p) REVERT: B 182 MET cc_start: 0.7865 (tmm) cc_final: 0.7483 (ttt) REVERT: B 236 ASN cc_start: 0.7268 (t0) cc_final: 0.6799 (t0) REVERT: C 32 ASP cc_start: 0.7793 (m-30) cc_final: 0.7440 (p0) REVERT: C 214 GLN cc_start: 0.6034 (pt0) cc_final: 0.5727 (pm20) REVERT: C 269 ASP cc_start: 0.5729 (t0) cc_final: 0.5158 (t0) REVERT: D 38 MET cc_start: 0.7730 (mmp) cc_final: 0.7445 (mmp) REVERT: D 210 LYS cc_start: 0.8216 (mttp) cc_final: 0.7982 (mmmt) REVERT: G 188 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7863 (mt-10) REVERT: H 205 PHE cc_start: 0.7012 (t80) cc_final: 0.6665 (t80) REVERT: H 227 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7636 (mp10) outliers start: 39 outliers final: 30 residues processed: 257 average time/residue: 0.1256 time to fit residues: 52.1193 Evaluate side-chains 254 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 289 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 214 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN C 17 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 ASN ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.165141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123512 restraints weight = 27439.876| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.80 r_work: 0.3056 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 20226 Z= 0.265 Angle : 0.685 8.745 27946 Z= 0.384 Chirality : 0.047 0.219 3197 Planarity : 0.005 0.046 3231 Dihedral : 16.960 178.194 3725 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.69 % Favored : 89.08 % Rotamer: Outliers : 2.88 % Allowed : 12.29 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.18), residues: 2218 helix: 0.84 (0.23), residues: 502 sheet: 0.57 (0.28), residues: 414 loop : -1.86 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 131 TYR 0.016 0.002 TYR A 86 PHE 0.036 0.003 PHE H 205 TRP 0.012 0.002 TRP G 239 HIS 0.006 0.002 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.27 (20226) covalent geometry : angle 0.68546 / 0.38 (27946) hydrogen bonds : bond 0.05508 / 3.64 ( 620) hydrogen bonds : angle 4.33364 / 2.90 ( 1750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 10 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.7882 (pt) REVERT: B 7 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.7162 (m) REVERT: B 26 MET cc_start: 0.8056 (mmm) cc_final: 0.7729 (tpt) REVERT: B 37 GLU cc_start: 0.7851 (tp30) cc_final: 0.7585 (tp30) REVERT: B 151 VAL cc_start: 0.6858 (p) cc_final: 0.6611 (p) REVERT: B 190 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: B 219 MET cc_start: 0.7148 (tpt) cc_final: 0.6870 (tpt) REVERT: C 3 LYS cc_start: 0.4127 (tptt) cc_final: 0.3702 (tttp) REVERT: C 32 ASP cc_start: 0.7877 (m-30) cc_final: 0.7492 (p0) REVERT: C 73 ASN cc_start: 0.5302 (p0) cc_final: 0.5085 (p0) REVERT: C 294 ASN cc_start: 0.7785 (m-40) cc_final: 0.7543 (m-40) REVERT: D 38 MET cc_start: 0.7892 (mmp) cc_final: 0.7577 (mmp) REVERT: D 210 LYS cc_start: 0.8187 (mttp) cc_final: 0.7912 (mmmt) REVERT: G 188 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8019 (mt-10) REVERT: H 207 GLU cc_start: 0.7223 (tp30) cc_final: 0.6919 (tp30) REVERT: H 250 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7410 (mt-10) outliers start: 53 outliers final: 38 residues processed: 265 average time/residue: 0.1298 time to fit residues: 55.2470 Evaluate side-chains 254 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 256 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 289 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 160 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 50 optimal weight: 0.0470 chunk 65 optimal weight: 0.0470 chunk 45 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 158 optimal weight: 0.0770 chunk 112 optimal weight: 0.8980 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN F 109 ASN H 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.171107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128822 restraints weight = 33779.351| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.25 r_work: 0.3139 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 20226 Z= 0.122 Angle : 0.563 9.283 27946 Z= 0.320 Chirality : 0.042 0.177 3197 Planarity : 0.004 0.041 3231 Dihedral : 16.827 177.740 3725 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.71 % Favored : 91.07 % Rotamer: Outliers : 1.85 % Allowed : 13.76 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.18), residues: 2218 helix: 1.20 (0.23), residues: 501 sheet: 0.88 (0.29), residues: 384 loop : -1.74 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 234 TYR 0.022 0.001 TYR C 262 PHE 0.022 0.001 PHE B 202 TRP 0.020 0.001 TRP F 130 HIS 0.002 0.001 HIS F 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (20226) covalent geometry : angle 0.56325 / 0.32 (27946) hydrogen bonds : bond 0.04105 / 2.77 ( 620) hydrogen bonds : angle 3.96554 / 2.64 ( 1750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: A 10 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.7851 (pt) REVERT: B 7 VAL cc_start: 0.7381 (OUTLIER) cc_final: 0.7145 (m) REVERT: B 26 MET cc_start: 0.8024 (mmm) cc_final: 0.7710 (tpt) REVERT: B 37 GLU cc_start: 0.7591 (tp30) cc_final: 0.7337 (tp30) REVERT: B 151 VAL cc_start: 0.6761 (p) cc_final: 0.6532 (p) REVERT: B 182 MET cc_start: 0.7861 (tmm) cc_final: 0.7497 (ttt) REVERT: B 190 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: B 219 MET cc_start: 0.6899 (tpt) cc_final: 0.6612 (tpt) REVERT: C 32 ASP cc_start: 0.8009 (m-30) cc_final: 0.7645 (p0) REVERT: C 73 ASN cc_start: 0.5657 (p0) cc_final: 0.5405 (p0) REVERT: C 191 MET cc_start: 0.7388 (mtm) cc_final: 0.6946 (mtp) REVERT: C 214 GLN cc_start: 0.6575 (pt0) cc_final: 0.6167 (pm20) REVERT: D 38 MET cc_start: 0.7826 (mmp) cc_final: 0.7508 (mmp) REVERT: D 210 LYS cc_start: 0.8262 (mttp) cc_final: 0.7967 (mmmt) REVERT: F 108 GLU cc_start: 0.5237 (OUTLIER) cc_final: 0.3900 (mt-10) REVERT: G 163 ASP cc_start: 0.7439 (t70) cc_final: 0.7211 (t70) REVERT: G 188 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8093 (mt-10) REVERT: H 207 GLU cc_start: 0.7017 (tp30) cc_final: 0.6694 (tp30) REVERT: H 227 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: H 250 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7269 (mt-10) outliers start: 34 outliers final: 24 residues processed: 254 average time/residue: 0.1272 time to fit residues: 52.0487 Evaluate side-chains 249 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 289 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 156 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN H 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.165607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.122211 restraints weight = 29661.717| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.67 r_work: 0.3068 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20226 Z= 0.240 Angle : 0.656 10.217 27946 Z= 0.367 Chirality : 0.046 0.245 3197 Planarity : 0.004 0.044 3231 Dihedral : 16.924 179.280 3725 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.42 % Favored : 89.31 % Rotamer: Outliers : 2.07 % Allowed : 13.87 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 2218 helix: 0.99 (0.23), residues: 501 sheet: 0.52 (0.28), residues: 414 loop : -1.83 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 133 TYR 0.014 0.002 TYR G 252 PHE 0.033 0.002 PHE H 205 TRP 0.013 0.002 TRP C 239 HIS 0.006 0.002 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (20226) covalent geometry : angle 0.65558 / 0.37 (27946) hydrogen bonds : bond 0.05023 / 3.33 ( 620) hydrogen bonds : angle 4.22759 / 2.82 ( 1750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: A 10 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7822 (pt) REVERT: A 58 GLU cc_start: 0.7577 (tt0) cc_final: 0.6831 (pm20) REVERT: B 26 MET cc_start: 0.8013 (mmm) cc_final: 0.7706 (tpt) REVERT: B 37 GLU cc_start: 0.7841 (tp30) cc_final: 0.7575 (tp30) REVERT: B 151 VAL cc_start: 0.6878 (p) cc_final: 0.6634 (p) REVERT: B 219 MET cc_start: 0.7167 (tpt) cc_final: 0.6898 (tpt) REVERT: C 32 ASP cc_start: 0.8029 (m-30) cc_final: 0.7694 (p0) REVERT: C 73 ASN cc_start: 0.5653 (p0) cc_final: 0.5400 (p0) REVERT: D 38 MET cc_start: 0.7920 (mmp) cc_final: 0.7558 (mmp) REVERT: D 210 LYS cc_start: 0.8119 (mttp) cc_final: 0.7885 (mmmt) REVERT: G 188 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8085 (mt-10) REVERT: H 207 GLU cc_start: 0.7231 (tp30) cc_final: 0.6919 (tp30) REVERT: H 227 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7702 (mp10) outliers start: 38 outliers final: 32 residues processed: 241 average time/residue: 0.1208 time to fit residues: 46.9143 Evaluate side-chains 242 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 289 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 74 optimal weight: 10.0000 chunk 68 optimal weight: 0.0030 chunk 63 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 161 optimal weight: 0.0070 overall best weight: 1.1612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN H 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.168448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125392 restraints weight = 35350.803| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.20 r_work: 0.3140 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20226 Z= 0.144 Angle : 0.588 9.027 27946 Z= 0.332 Chirality : 0.043 0.245 3197 Planarity : 0.004 0.044 3231 Dihedral : 16.870 178.862 3725 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.83 % Favored : 89.94 % Rotamer: Outliers : 1.79 % Allowed : 14.46 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 2218 helix: 1.14 (0.23), residues: 501 sheet: 0.57 (0.28), residues: 414 loop : -1.80 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 234 TYR 0.016 0.001 TYR A 86 PHE 0.025 0.001 PHE B 202 TRP 0.016 0.001 TRP F 130 HIS 0.003 0.001 HIS F 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (20226) covalent geometry : angle 0.58847 / 0.33 (27946) hydrogen bonds : bond 0.04283 / 2.88 ( 620) hydrogen bonds : angle 4.07313 / 2.71 ( 1750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: A 10 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.7830 (pt) REVERT: A 58 GLU cc_start: 0.7513 (tt0) cc_final: 0.6756 (pm20) REVERT: B 26 MET cc_start: 0.8030 (mmm) cc_final: 0.7745 (tpt) REVERT: B 37 GLU cc_start: 0.7866 (tp30) cc_final: 0.7607 (tp30) REVERT: B 151 VAL cc_start: 0.6831 (p) cc_final: 0.6603 (p) REVERT: B 182 MET cc_start: 0.8011 (tmm) cc_final: 0.7709 (ttt) REVERT: B 219 MET cc_start: 0.7180 (tpt) cc_final: 0.6915 (tpt) REVERT: C 32 ASP cc_start: 0.8040 (m-30) cc_final: 0.7697 (p0) REVERT: C 73 ASN cc_start: 0.5631 (p0) cc_final: 0.5383 (p0) REVERT: C 214 GLN cc_start: 0.6796 (pt0) cc_final: 0.6220 (pm20) REVERT: D 38 MET cc_start: 0.7991 (mmp) cc_final: 0.7641 (mmp) REVERT: D 210 LYS cc_start: 0.8115 (mttp) cc_final: 0.7882 (mmmt) REVERT: G 188 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8122 (mt-10) REVERT: H 207 GLU cc_start: 0.7282 (tp30) cc_final: 0.7008 (tp30) REVERT: H 250 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7874 (mt-10) outliers start: 33 outliers final: 28 residues processed: 235 average time/residue: 0.1281 time to fit residues: 48.1289 Evaluate side-chains 239 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 289 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 114 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 197 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.168938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126182 restraints weight = 27318.764| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.44 r_work: 0.3154 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20226 Z= 0.141 Angle : 0.575 8.956 27946 Z= 0.326 Chirality : 0.042 0.190 3197 Planarity : 0.004 0.043 3231 Dihedral : 16.858 179.213 3725 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.70 % Favored : 90.12 % Rotamer: Outliers : 2.18 % Allowed : 14.14 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2218 helix: 1.36 (0.23), residues: 483 sheet: 0.59 (0.28), residues: 414 loop : -1.69 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 234 TYR 0.016 0.001 TYR A 86 PHE 0.024 0.001 PHE B 202 TRP 0.017 0.001 TRP C 239 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (20226) covalent geometry : angle 0.57513 / 0.33 (27946) hydrogen bonds : bond 0.04134 / 2.78 ( 620) hydrogen bonds : angle 3.97939 / 2.64 ( 1750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5227.86 seconds wall clock time: 90 minutes 8.00 seconds (5408.00 seconds total)