Starting phenix.real_space_refine on Sun Sep 13 08:26:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wwv_32874/09_2026/7wwv_32874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwv_32874/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wwv_32874/09_2026/7wwv_32874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwv_32874/09_2026/7wwv_32874.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wwv_32874/09_2026/7wwv_32874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwv_32874/09_2026/7wwv_32874.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wwv_32874/09_2026/7wwv_32874.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wwv_32874/09_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-2.2.1-6174/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: {'RNAv2': 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: 5.87, per 1000 atoms: 0.30 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: 1.87 Conformation dependent library (CDL) restraints added in 953.6 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: 2.51 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: 3.37 Time building geometry restraints manager: 2.49 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: 27200 1.88 - 3.76: 670 3.76 - 5.64: 66 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 - 28.18: 10962 28.18 - 56.36: 591 56.36 - 84.54: 129 84.54 - 112.72: 6 112.72 - 140.90: 1 Dihedral angle restraints: 11689 sinusoidal: 5309 harmonic: 6380 Sorted by residual: dihedral pdb=" C4' G M 9 " pdb=" C3' G M 9 " pdb=" C2' G M 9 " pdb=" C1' G M 9 " ideal model delta sinusoidal sigma weight residual 36.34 -36.86 73.21 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' U M 25 " pdb=" C3' U M 25 " pdb=" C2' U M 25 " pdb=" C1' U M 25 " ideal model delta sinusoidal sigma weight residual 36.34 -36.62 72.97 1 3.10e+00 1.04e-01 7.06e+02 dihedral pdb=" C4' A M 13 " pdb=" C3' A M 13 " pdb=" C2' A M 13 " pdb=" C1' A M 13 " ideal model delta sinusoidal sigma weight residual 36.34 -36.48 72.82 1 3.10e+00 1.04e-01 7.04e+02 ... (remaining 11686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2667 0.057 - 0.115: 408 0.115 - 0.172: 36 0.172 - 0.230: 24 0.230 - 0.287: 62 Chirality restraints: 3197 Sorted by residual: chirality pdb=" C2' A M 8 " pdb=" C3' A M 8 " pdb=" O2' A M 8 " pdb=" C1' A M 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C2' U M 34 " pdb=" C3' U M 34 " pdb=" O2' U M 34 " pdb=" C1' U M 34 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' C M 30 " pdb=" C3' C M 30 " pdb=" O2' C M 30 " pdb=" C1' C M 30 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (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: 0.770 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: 0.030 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.680 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.460 ------------------------------------------------------------------------------- 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= 0.235 Angle : 0.667 9.395 27946 Z= 0.436 Chirality : 0.056 0.287 3197 Planarity : 0.003 0.042 3231 Dihedral : 16.997 140.898 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 0.00292 / 0.23 (20226) covalent geometry : angle 0.66719 / 0.44 (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 : 0.706 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: 0.1304 time to fit residues: 64.2207 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 : 0.606 ------------------------------------------------------------------------------- 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: 0.0010 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: 0.9790 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134735 restraints weight = 29831.804| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.65 r_work: 0.3334 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20226 Z= 0.173 Angle : 1.012 22.562 27946 Z= 0.441 Chirality : 0.092 1.245 3197 Planarity : 0.004 0.040 3231 Dihedral : 16.385 146.194 3725 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.89 % Favored : 91.07 % Rotamer: Outliers : 1.03 % Allowed : 6.91 % Favored : 92.06 % 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 (0.19), residues: 2218 helix: 1.23 (0.23), residues: 498 sheet: 1.44 (0.31), residues: 372 loop : -1.74 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 263 TYR 0.016 0.001 TYR D 240 PHE 0.015 0.001 PHE B 202 TRP 0.017 0.001 TRP C 239 HIS 0.003 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (20226) covalent geometry : angle 1.01186 / 0.44 (27946) hydrogen bonds : bond 0.05414 / 3.63 ( 620) hydrogen bonds : angle 4.31777 / 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 275 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 174 GLU cc_start: 0.7430 (pp20) cc_final: 0.6701 (tm-30) REVERT: B 48 LYS cc_start: 0.7818 (mmmt) cc_final: 0.7433 (mptt) REVERT: B 236 ASN cc_start: 0.7138 (t0) cc_final: 0.6617 (t0) REVERT: H 207 GLU cc_start: 0.6612 (tp30) cc_final: 0.6382 (tp30) REVERT: H 274 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8456 (mtp) outliers start: 19 outliers final: 11 residues processed: 265 average time/residue: 0.1335 time to fit residues: 57.0989 Evaluate side-chains 235 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 223 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 44 VAL 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 H residue 274 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 90 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 120 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 150 optimal weight: 0.0670 chunk 195 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN C 27 ASN E 203 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.176200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.135615 restraints weight = 34120.254| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.13 r_work: 0.3255 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20226 Z= 0.139 Angle : 0.751 15.853 27946 Z= 0.357 Chirality : 0.067 0.992 3197 Planarity : 0.003 0.039 3231 Dihedral : 16.763 159.846 3725 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.84 % Favored : 90.98 % Rotamer: Outliers : 1.36 % Allowed : 9.08 % Favored : 89.56 % 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: -0.58 (0.19), residues: 2218 helix: 1.36 (0.23), residues: 493 sheet: 1.12 (0.29), residues: 413 loop : -1.70 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 263 TYR 0.027 0.001 TYR A 86 PHE 0.017 0.001 PHE B 202 TRP 0.014 0.001 TRP F 130 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (20226) covalent geometry : angle 0.75130 / 0.36 (27946) hydrogen bonds : bond 0.04531 / 2.95 ( 620) hydrogen bonds : angle 4.08154 / 2.69 ( 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 271 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 246 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.6923 (tttt) cc_final: 0.6666 (tttt) REVERT: A 7 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: B 26 MET cc_start: 0.7921 (mmm) cc_final: 0.7658 (tpp) REVERT: B 48 LYS cc_start: 0.7758 (mmmt) cc_final: 0.6920 (mtpp) REVERT: B 236 ASN cc_start: 0.7094 (t0) cc_final: 0.6564 (t0) REVERT: D 38 MET cc_start: 0.7872 (mmp) cc_final: 0.7665 (mmp) REVERT: G 188 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8032 (mt-10) REVERT: H 207 GLU cc_start: 0.6795 (tp30) cc_final: 0.6552 (tp30) REVERT: H 274 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8459 (mtp) outliers start: 25 outliers final: 18 residues processed: 262 average time/residue: 0.1326 time to fit residues: 55.4893 Evaluate side-chains 246 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 67 ASN 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 176 VAL Chi-restraints excluded: chain E residue 88 ASP 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 255 VAL Chi-restraints excluded: chain H residue 274 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 170 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 201 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 74 GLN C 279 ASN D 17 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN E 203 GLN ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 ASN F 214 GLN H 227 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.169517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126905 restraints weight = 35580.273| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.39 r_work: 0.3112 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20226 Z= 0.221 Angle : 0.802 15.867 27946 Z= 0.391 Chirality : 0.067 0.791 3197 Planarity : 0.004 0.042 3231 Dihedral : 17.036 159.777 3725 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.10 % Favored : 89.67 % Rotamer: Outliers : 2.45 % Allowed : 9.84 % Favored : 87.71 % 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: -0.86 (0.18), residues: 2218 helix: 1.04 (0.23), residues: 500 sheet: 0.96 (0.29), residues: 384 loop : -1.80 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 14 TYR 0.013 0.002 TYR D 240 PHE 0.034 0.002 PHE H 205 TRP 0.015 0.002 TRP A 63 HIS 0.005 0.002 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (20226) covalent geometry : angle 0.80231 / 0.39 (27946) hydrogen bonds : bond 0.04718 / 3.06 ( 620) hydrogen bonds : angle 4.23048 / 2.82 ( 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 278 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.6888 (tttt) cc_final: 0.6596 (tttt) REVERT: A 7 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: A 10 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.7925 (pt) REVERT: B 26 MET cc_start: 0.7905 (mmm) cc_final: 0.7447 (tpt) REVERT: B 37 GLU cc_start: 0.7819 (tp30) cc_final: 0.7593 (tp30) REVERT: B 236 ASN cc_start: 0.7347 (t0) cc_final: 0.6908 (t0) REVERT: C 294 ASN cc_start: 0.7556 (m-40) cc_final: 0.7333 (m-40) REVERT: D 38 MET cc_start: 0.7849 (mmp) cc_final: 0.7624 (mmp) REVERT: D 210 LYS cc_start: 0.8235 (mttp) cc_final: 0.7940 (mmmt) REVERT: E 63 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8381 (mm-40) REVERT: G 188 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7999 (mt-10) REVERT: G 191 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7854 (mpp) REVERT: H 207 GLU cc_start: 0.7104 (tp30) cc_final: 0.6737 (tp30) REVERT: H 274 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8497 (mtp) outliers start: 45 outliers final: 28 residues processed: 263 average time/residue: 0.1357 time to fit residues: 57.1654 Evaluate side-chains 251 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 54 ILE Chi-restraints excluded: chain A residue 86 TYR 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 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 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 G residue 191 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 268 THR Chi-restraints excluded: chain H residue 274 MET Chi-restraints excluded: chain H residue 289 MET 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: 3.9990 chunk 208 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 230 optimal weight: 30.0000 chunk 85 optimal weight: 0.5980 chunk 206 optimal weight: 7.9990 chunk 196 optimal weight: 0.0970 chunk 111 optimal weight: 0.0020 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN C 17 ASN C 146 ASN C 279 ASN D 203 GLN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 ASN E 203 GLN F 109 ASN F 294 ASN H 227 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.131626 restraints weight = 27968.920| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.43 r_work: 0.3247 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20226 Z= 0.130 Angle : 0.710 15.150 27946 Z= 0.347 Chirality : 0.058 0.663 3197 Planarity : 0.003 0.039 3231 Dihedral : 16.922 163.094 3725 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.93 % Favored : 90.89 % Rotamer: Outliers : 2.23 % Allowed : 11.42 % Favored : 86.35 % 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: -0.70 (0.18), residues: 2218 helix: 1.31 (0.23), residues: 495 sheet: 0.71 (0.27), residues: 456 loop : -1.75 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 234 TYR 0.018 0.001 TYR C 262 PHE 0.018 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 0.00250 / 0.13 (20226) covalent geometry : angle 0.70981 / 0.35 (27946) hydrogen bonds : bond 0.03970 / 2.54 ( 620) hydrogen bonds : angle 3.98485 / 2.64 ( 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 275 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.6902 (tttt) cc_final: 0.6606 (tttt) REVERT: A 7 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 10 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.7869 (pt) REVERT: B 26 MET cc_start: 0.7630 (mmm) cc_final: 0.7101 (tpt) REVERT: B 37 GLU cc_start: 0.7574 (tp30) cc_final: 0.7316 (tp30) REVERT: B 151 VAL cc_start: 0.6945 (p) cc_final: 0.6713 (p) REVERT: B 182 MET cc_start: 0.7543 (ttt) cc_final: 0.6883 (ttt) REVERT: B 219 MET cc_start: 0.6869 (tpt) cc_final: 0.6566 (tpt) REVERT: B 236 ASN cc_start: 0.7279 (t0) cc_final: 0.6867 (t0) REVERT: C 32 ASP cc_start: 0.7785 (m-30) cc_final: 0.7436 (p0) REVERT: C 214 GLN cc_start: 0.6039 (pt0) cc_final: 0.5716 (pm20) REVERT: C 294 ASN cc_start: 0.7433 (m-40) cc_final: 0.7199 (m-40) REVERT: D 38 MET cc_start: 0.7587 (mmp) cc_final: 0.7291 (mmp) REVERT: D 210 LYS cc_start: 0.8174 (mttp) cc_final: 0.7933 (mmmt) REVERT: E 53 ASN cc_start: 0.8265 (t0) cc_final: 0.8036 (t0) REVERT: G 188 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7847 (mt-10) REVERT: H 274 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8420 (mtp) outliers start: 41 outliers final: 25 residues processed: 261 average time/residue: 0.1315 time to fit residues: 55.1066 Evaluate side-chains 247 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 95 ASP Chi-restraints excluded: chain B residue 190 GLU 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 128 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 13 SER 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 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 G residue 187 VAL 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 274 MET 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: 1.9990 chunk 227 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 230 optimal weight: 40.0000 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN C 146 ASN C 279 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN H 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.169044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126925 restraints weight = 27813.960| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.64 r_work: 0.3146 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20226 Z= 0.197 Angle : 0.767 15.289 27946 Z= 0.378 Chirality : 0.062 0.689 3197 Planarity : 0.004 0.043 3231 Dihedral : 16.989 164.785 3725 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.33 % Favored : 89.45 % Rotamer: Outliers : 2.50 % Allowed : 12.13 % Favored : 85.37 % 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: 1.07 (0.23), residues: 501 sheet: 0.86 (0.29), residues: 384 loop : -1.82 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 234 TYR 0.016 0.002 TYR A 86 PHE 0.026 0.002 PHE H 205 TRP 0.010 0.002 TRP C 239 HIS 0.004 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (20226) covalent geometry : angle 0.76727 / 0.38 (27946) hydrogen bonds : bond 0.04477 / 2.88 ( 620) hydrogen bonds : angle 4.13839 / 2.76 ( 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: 46 poor density : 226 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.6837 (tttt) cc_final: 0.6473 (tttt) REVERT: A 7 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: A 10 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.7853 (pt) REVERT: B 37 GLU cc_start: 0.7817 (tp30) cc_final: 0.7559 (tp30) REVERT: B 151 VAL cc_start: 0.6814 (p) cc_final: 0.6570 (p) REVERT: B 182 MET cc_start: 0.7770 (ttt) cc_final: 0.7114 (ttt) REVERT: B 190 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: B 219 MET cc_start: 0.6976 (tpt) cc_final: 0.6679 (tpt) REVERT: C 32 ASP cc_start: 0.7836 (m-30) cc_final: 0.7472 (p0) REVERT: C 73 ASN cc_start: 0.5312 (p0) cc_final: 0.5098 (p0) REVERT: D 38 MET cc_start: 0.7803 (mmp) cc_final: 0.7483 (mmp) REVERT: D 210 LYS cc_start: 0.8084 (mttp) cc_final: 0.7842 (mmmt) REVERT: G 188 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8024 (mt-10) REVERT: H 250 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7337 (mt-10) REVERT: H 274 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8505 (mtp) outliers start: 46 outliers final: 36 residues processed: 258 average time/residue: 0.1331 time to fit residues: 55.1107 Evaluate side-chains 255 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 54 ILE 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 128 THR 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 E residue 13 SER Chi-restraints excluded: chain E residue 281 LYS 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 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 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 256 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 MET 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: 6.9990 chunk 196 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 223 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.170437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.128551 restraints weight = 27396.234| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.39 r_work: 0.3186 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20226 Z= 0.165 Angle : 0.731 15.294 27946 Z= 0.362 Chirality : 0.058 0.657 3197 Planarity : 0.004 0.048 3231 Dihedral : 17.015 166.368 3725 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.88 % Favored : 89.94 % Rotamer: Outliers : 2.61 % Allowed : 13.00 % 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: -0.88 (0.18), residues: 2218 helix: 1.15 (0.23), residues: 501 sheet: 0.57 (0.27), residues: 444 loop : -1.85 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 234 TYR 0.014 0.001 TYR D 240 PHE 0.022 0.001 PHE B 202 TRP 0.014 0.001 TRP F 130 HIS 0.004 0.001 HIS F 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (20226) covalent geometry : angle 0.73096 / 0.36 (27946) hydrogen bonds : bond 0.04098 / 2.62 ( 620) hydrogen bonds : angle 4.07201 / 2.71 ( 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 273 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.6920 (tttt) cc_final: 0.6530 (tttt) REVERT: A 7 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: A 10 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.7854 (pt) REVERT: A 58 GLU cc_start: 0.7461 (tt0) cc_final: 0.6716 (pm20) REVERT: B 7 VAL cc_start: 0.7339 (OUTLIER) cc_final: 0.7135 (m) REVERT: B 37 GLU cc_start: 0.7796 (tp30) cc_final: 0.7524 (tp30) REVERT: B 151 VAL cc_start: 0.6827 (p) cc_final: 0.6578 (p) REVERT: B 182 MET cc_start: 0.7623 (ttt) cc_final: 0.6947 (ttt) REVERT: B 190 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: B 219 MET cc_start: 0.6888 (tpt) cc_final: 0.6604 (tpt) REVERT: C 32 ASP cc_start: 0.7929 (m-30) cc_final: 0.7643 (p0) REVERT: C 73 ASN cc_start: 0.5607 (p0) cc_final: 0.5356 (p0) REVERT: C 191 MET cc_start: 0.7426 (mtm) cc_final: 0.6829 (mtp) REVERT: C 214 GLN cc_start: 0.6671 (pt0) cc_final: 0.6153 (pm20) REVERT: D 38 MET cc_start: 0.7793 (mmp) cc_final: 0.7434 (mmp) REVERT: D 210 LYS cc_start: 0.8053 (mttp) cc_final: 0.7834 (mmmt) REVERT: F 129 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7402 (pt) REVERT: G 188 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7977 (mt-10) REVERT: G 191 MET cc_start: 0.8175 (mpp) cc_final: 0.6636 (mpp) REVERT: H 250 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7239 (mt-10) REVERT: H 274 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8404 (mtp) outliers start: 48 outliers final: 36 residues processed: 261 average time/residue: 0.1346 time to fit residues: 56.5314 Evaluate side-chains 259 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 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 281 LYS Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 129 LEU 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 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 247 ILE 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 199 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 274 MET 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: 1.9990 chunk 75 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.168220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124793 restraints weight = 33714.232| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.13 r_work: 0.3103 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20226 Z= 0.217 Angle : 0.780 15.472 27946 Z= 0.385 Chirality : 0.061 0.692 3197 Planarity : 0.004 0.043 3231 Dihedral : 17.132 165.043 3725 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.19 % Favored : 89.54 % Rotamer: Outliers : 2.72 % Allowed : 13.43 % Favored : 83.85 % 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: 0.95 (0.23), residues: 501 sheet: 0.49 (0.28), residues: 414 loop : -1.87 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 133 TYR 0.017 0.002 TYR A 86 PHE 0.022 0.002 PHE E 205 TRP 0.012 0.002 TRP C 239 HIS 0.005 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (20226) covalent geometry : angle 0.77996 / 0.39 (27946) hydrogen bonds : bond 0.04514 / 2.90 ( 620) hydrogen bonds : angle 4.20116 / 2.81 ( 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 267 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.6825 (tttt) cc_final: 0.6436 (tttt) REVERT: A 7 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: A 10 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.7895 (pt) REVERT: A 58 GLU cc_start: 0.7494 (tt0) cc_final: 0.6676 (pm20) REVERT: B 37 GLU cc_start: 0.7841 (tp30) cc_final: 0.7580 (tp30) REVERT: B 151 VAL cc_start: 0.6822 (p) cc_final: 0.6586 (p) REVERT: B 182 MET cc_start: 0.7679 (ttt) cc_final: 0.7063 (ttt) REVERT: B 190 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: B 219 MET cc_start: 0.7070 (tpt) cc_final: 0.6800 (tpt) REVERT: C 32 ASP cc_start: 0.8003 (m-30) cc_final: 0.7678 (p0) REVERT: C 73 ASN cc_start: 0.5626 (p0) cc_final: 0.5391 (p0) REVERT: C 191 MET cc_start: 0.7447 (mtm) cc_final: 0.6887 (mtp) REVERT: D 38 MET cc_start: 0.7901 (mmp) cc_final: 0.7535 (mmp) REVERT: D 210 LYS cc_start: 0.8104 (mttp) cc_final: 0.7857 (mmmt) REVERT: G 188 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8108 (mt-10) REVERT: H 227 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7948 (mp10) REVERT: H 274 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8277 (mtp) outliers start: 50 outliers final: 37 residues processed: 256 average time/residue: 0.1340 time to fit residues: 55.3124 Evaluate side-chains 252 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 139 THR 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 128 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 281 LYS 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 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 G residue 274 MET Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 199 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 274 MET 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: 0.9990 chunk 125 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 196 optimal weight: 0.0060 chunk 178 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 115 optimal weight: 0.0370 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 overall best weight: 0.8080 ------------------------------------------------------------------------------- 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 G 63 GLN H 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.171505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129087 restraints weight = 29718.182| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.61 r_work: 0.3185 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20226 Z= 0.131 Angle : 0.711 15.141 27946 Z= 0.352 Chirality : 0.056 0.632 3197 Planarity : 0.004 0.043 3231 Dihedral : 17.072 166.317 3725 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.70 % Favored : 90.12 % Rotamer: Outliers : 2.66 % Allowed : 13.65 % 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: -0.83 (0.18), residues: 2218 helix: 1.30 (0.23), residues: 483 sheet: 0.52 (0.27), residues: 444 loop : -1.77 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 133 TYR 0.019 0.001 TYR A 86 PHE 0.024 0.001 PHE B 202 TRP 0.019 0.001 TRP F 130 HIS 0.003 0.001 HIS F 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (20226) covalent geometry : angle 0.71091 / 0.35 (27946) hydrogen bonds : bond 0.03883 / 2.47 ( 620) hydrogen bonds : angle 4.02161 / 2.68 ( 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 270 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.6608 (tttt) cc_final: 0.6274 (tttt) REVERT: A 7 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: A 10 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7813 (pt) REVERT: A 58 GLU cc_start: 0.7470 (tt0) cc_final: 0.6695 (pm20) REVERT: B 37 GLU cc_start: 0.7803 (tp30) cc_final: 0.7527 (tp30) REVERT: B 151 VAL cc_start: 0.6756 (p) cc_final: 0.6529 (p) REVERT: B 182 MET cc_start: 0.7614 (ttt) cc_final: 0.6943 (ttt) REVERT: B 219 MET cc_start: 0.6822 (tpt) cc_final: 0.6545 (tpt) REVERT: C 32 ASP cc_start: 0.7961 (m-30) cc_final: 0.7661 (p0) REVERT: C 73 ASN cc_start: 0.5617 (p0) cc_final: 0.5361 (p0) REVERT: C 191 MET cc_start: 0.7394 (mtm) cc_final: 0.6835 (mtp) REVERT: C 214 GLN cc_start: 0.6686 (pt0) cc_final: 0.6154 (pm20) REVERT: D 38 MET cc_start: 0.7823 (mmp) cc_final: 0.7446 (mmp) REVERT: D 210 LYS cc_start: 0.8051 (mttp) cc_final: 0.7824 (mmmt) REVERT: F 108 GLU cc_start: 0.5313 (OUTLIER) cc_final: 0.3915 (mt-10) REVERT: G 188 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8006 (mt-10) REVERT: H 227 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: H 274 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8238 (mtp) outliers start: 49 outliers final: 37 residues processed: 258 average time/residue: 0.1271 time to fit residues: 53.3902 Evaluate side-chains 259 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 78 ASN Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 170 ILE 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 169 ILE 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 128 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 281 LYS 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 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 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 274 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: 10.0000 chunk 63 optimal weight: 3.9990 chunk 215 optimal weight: 0.0980 chunk 45 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 161 optimal weight: 0.0270 overall best weight: 0.9842 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.171386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128720 restraints weight = 35355.880| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.12 r_work: 0.3152 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 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 = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20226 Z= 0.138 Angle : 0.706 14.867 27946 Z= 0.350 Chirality : 0.056 0.622 3197 Planarity : 0.004 0.043 3231 Dihedral : 17.052 167.404 3725 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.79 % Favored : 90.03 % Rotamer: Outliers : 2.45 % Allowed : 14.08 % Favored : 83.47 % 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: -0.79 (0.18), residues: 2218 helix: 1.34 (0.23), residues: 483 sheet: 0.54 (0.27), residues: 444 loop : -1.76 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 133 TYR 0.018 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 0.00279 / 0.14 (20226) covalent geometry : angle 0.70560 / 0.35 (27946) hydrogen bonds : bond 0.03793 / 2.40 ( 620) hydrogen bonds : angle 3.97129 / 2.64 ( 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 266 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.6551 (tttt) cc_final: 0.6241 (tttt) REVERT: A 7 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: A 10 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7788 (pt) REVERT: A 58 GLU cc_start: 0.7521 (tt0) cc_final: 0.6654 (pm20) REVERT: B 7 VAL cc_start: 0.7373 (OUTLIER) cc_final: 0.7165 (m) REVERT: B 37 GLU cc_start: 0.7841 (tp30) cc_final: 0.7570 (tp30) REVERT: B 151 VAL cc_start: 0.6751 (p) cc_final: 0.6527 (p) REVERT: B 182 MET cc_start: 0.7698 (ttt) cc_final: 0.7074 (ttt) REVERT: B 219 MET cc_start: 0.6910 (tpt) cc_final: 0.6638 (tpt) REVERT: C 32 ASP cc_start: 0.7994 (m-30) cc_final: 0.7650 (p0) REVERT: C 73 ASN cc_start: 0.5606 (p0) cc_final: 0.5358 (p0) REVERT: C 191 MET cc_start: 0.7401 (mtm) cc_final: 0.6859 (mtp) REVERT: C 214 GLN cc_start: 0.6706 (pt0) cc_final: 0.6172 (pm20) REVERT: D 38 MET cc_start: 0.7901 (mmp) cc_final: 0.7527 (mmp) REVERT: D 210 LYS cc_start: 0.8084 (mttp) cc_final: 0.7833 (mmmt) REVERT: F 108 GLU cc_start: 0.5412 (OUTLIER) cc_final: 0.3953 (mt-10) REVERT: G 188 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8094 (mt-10) REVERT: H 227 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7697 (mp10) REVERT: H 274 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8422 (mtp) outliers start: 45 outliers final: 36 residues processed: 254 average time/residue: 0.1297 time to fit residues: 53.2591 Evaluate side-chains 260 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 170 ILE 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 169 ILE 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 128 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 129 LEU 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 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 199 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 274 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: 0.0030 chunk 197 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 209 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 92 optimal weight: 0.0470 chunk 94 optimal weight: 0.6980 overall best weight: 0.4490 ------------------------------------------------------------------------------- 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 H 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131893 restraints weight = 27329.498| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.35 r_work: 0.3244 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20226 Z= 0.120 Angle : 0.677 14.387 27946 Z= 0.338 Chirality : 0.053 0.580 3197 Planarity : 0.004 0.046 3231 Dihedral : 17.001 168.325 3725 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.34 % Favored : 90.48 % Rotamer: Outliers : 2.23 % Allowed : 14.46 % Favored : 83.31 % 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: 1.48 (0.24), residues: 483 sheet: 0.54 (0.27), residues: 456 loop : -1.71 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 133 TYR 0.018 0.001 TYR A 86 PHE 0.025 0.001 PHE B 202 TRP 0.021 0.001 TRP F 130 HIS 0.002 0.001 HIS H 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 (20226) covalent geometry : angle 0.67713 / 0.34 (27946) hydrogen bonds : bond 0.03599 / 2.25 ( 620) hydrogen bonds : angle 3.86021 / 2.57 ( 1750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5533.46 seconds wall clock time: 95 minutes 14.81 seconds (5714.81 seconds total)