Starting phenix.real_space_refine on Thu Jun 19 04:08:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwv_32874/06_2025/7wwv_32874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwv_32874/06_2025/7wwv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wwv_32874/06_2025/7wwv_32874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwv_32874/06_2025/7wwv_32874.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwv_32874/06_2025/7wwv_32874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwv_32874/06_2025/7wwv_32874.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19622 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1431 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain: "B" Number of atoms: 1924 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1919 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 237} Conformer: "B" Number of residues, atoms: 248, 1919 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 237} bond proxies already assigned to first conformer: 1950 Chain: "C" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 811 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 15, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 22, 'rna3p': 16} Chain: "O" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 952 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "N" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 662 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Time building chain proxies: 12.80, per 1000 atoms: 0.65 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: 5.21 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 6.97 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: 5.97 Time building geometry restraints manager: 5.83 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=" CA THR G 244 " pdb=" C THR G 244 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.34e-02 5.57e+03 1.13e+00 bond pdb=" CA GLU D 108 " pdb=" CB GLU D 108 " ideal model delta sigma weight residual 1.530 1.548 -0.017 1.69e-02 3.50e+03 1.07e+00 bond pdb=" CA GLU F 108 " pdb=" CB GLU F 108 " ideal model delta sigma weight residual 1.530 1.548 -0.017 1.69e-02 3.50e+03 1.07e+00 bond pdb=" CB GLU H 286 " pdb=" CG GLU H 286 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.63e-01 bond pdb=" CA GLU C 108 " pdb=" CB GLU C 108 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.51e-02 4.39e+03 8.28e-01 ... (remaining 20221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 27506 1.88 - 3.76: 410 3.76 - 5.64: 20 5.64 - 7.52: 7 7.52 - 9.39: 3 Bond angle restraints: 27946 Sorted by residual: 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=" N PRO F 246 " pdb=" CA PRO F 246 " pdb=" C PRO F 246 " ideal model delta sigma weight residual 111.33 116.15 -4.82 1.43e+00 4.89e-01 1.14e+01 angle pdb=" N PRO E 246 " pdb=" CA PRO E 246 " pdb=" C PRO E 246 " ideal model delta sigma weight residual 111.33 116.00 -4.67 1.43e+00 4.89e-01 1.07e+01 ... (remaining 27941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 11356 35.63 - 71.26: 409 71.26 - 106.88: 39 106.88 - 142.51: 1 142.51 - 178.14: 2 Dihedral angle restraints: 11807 sinusoidal: 5427 harmonic: 6380 Sorted by residual: dihedral pdb=" O4' U M 32 " pdb=" C1' U M 32 " pdb=" N1 U M 32 " pdb=" C2 U M 32 " ideal model delta sinusoidal sigma weight residual -128.00 50.14 -178.14 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 3 " pdb=" C1' U M 3 " pdb=" N1 U M 3 " pdb=" C2 U M 3 " ideal model delta sinusoidal sigma weight residual -128.00 48.57 -176.57 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 35 " pdb=" C1' U M 35 " pdb=" N1 U M 35 " pdb=" C2 U M 35 " ideal model delta sinusoidal sigma weight residual -160.00 -99.63 -60.37 1 1.50e+01 4.44e-03 2.16e+01 ... (remaining 11804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2405 0.039 - 0.077: 603 0.077 - 0.116: 153 0.116 - 0.155: 32 0.155 - 0.193: 4 Chirality restraints: 3197 Sorted by residual: chirality pdb=" CB THR F 268 " pdb=" CA THR F 268 " pdb=" OG1 THR F 268 " pdb=" CG2 THR F 268 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CB THR D 268 " pdb=" CA THR D 268 " pdb=" OG1 THR D 268 " pdb=" CG2 THR D 268 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CB THR G 268 " pdb=" CA THR G 268 " pdb=" OG1 THR G 268 " pdb=" CG2 THR G 268 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.00e-01 ... (remaining 3194 not shown) Planarity restraints: 3231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 239 " -0.015 2.00e-02 2.50e+03 1.27e-02 4.02e+00 pdb=" CG TRP C 239 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 239 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 239 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 239 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 239 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 239 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 239 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 239 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 156 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 157 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 159 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C GLU G 159 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU G 159 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE G 160 " 0.009 2.00e-02 2.50e+03 ... (remaining 3228 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1452 2.74 - 3.28: 18514 3.28 - 3.82: 30570 3.82 - 4.36: 36717 4.36 - 4.90: 63982 Nonbonded interactions: 151235 Sorted by model distance: nonbonded pdb=" O ALA H 45 " pdb=" O2' A M 13 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASP F 226 " pdb=" NE2 GLN F 227 " model vdw 2.242 3.120 nonbonded pdb=" OH TYR H 117 " pdb=" O ASP H 161 " model vdw 2.243 3.040 nonbonded pdb=" O ALA D 45 " pdb=" O2' A M 37 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR F 117 " pdb=" O ASP F 161 " model vdw 2.246 3.040 ... (remaining 151230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 49.650 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.002 0.028 20226 Z= 0.117 Angle : 0.568 9.395 27946 Z= 0.346 Chirality : 0.038 0.193 3197 Planarity : 0.003 0.042 3231 Dihedral : 16.776 178.140 7733 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.034 0.001 TRP C 239 HIS 0.002 0.001 HIS E 189 PHE 0.021 0.001 PHE E 90 TYR 0.019 0.001 TYR D 240 ARG 0.003 0.000 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.17787 ( 620) hydrogen bonds : angle 6.54922 ( 1750) covalent geometry : bond 0.00212 (20226) covalent geometry : angle 0.56765 (27946) *********************** 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 : 2.039 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: 0.7450 (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: 0.6976 (mt-10) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2810 time to fit residues: 136.2478 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 : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN B 74 GLN C 279 ASN D 17 ASN ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN H 20 ASN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.167607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126714 restraints weight = 29690.592| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.62 r_work: 0.3180 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20226 Z= 0.200 Angle : 0.627 11.356 27946 Z= 0.344 Chirality : 0.043 0.178 3197 Planarity : 0.004 0.044 3231 Dihedral : 18.108 178.025 3843 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.74 % Favored : 90.03 % Rotamer: Outliers : 1.14 % Allowed : 7.88 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 2218 helix: 1.11 (0.23), residues: 497 sheet: 1.07 (0.30), residues: 402 loop : -1.80 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 239 HIS 0.006 0.002 HIS E 189 PHE 0.025 0.002 PHE H 205 TYR 0.016 0.002 TYR D 240 ARG 0.006 0.001 ARG E 14 Details of bonding type rmsd hydrogen bonds : bond 0.05102 ( 620) hydrogen bonds : angle 4.33781 ( 1750) covalent geometry : bond 0.00460 (20226) covalent geometry : angle 0.62728 (27946) *********************** 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 258 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 1.908 Fit side-chains REVERT: B 236 ASN cc_start: 0.7270 (t0) cc_final: 0.6846 (t0) REVERT: D 210 LYS cc_start: 0.8077 (mttp) cc_final: 0.7851 (mmmt) REVERT: G 109 ASN cc_start: 0.7903 (t0) cc_final: 0.7513 (t0) REVERT: G 188 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8024 (mt-10) REVERT: H 172 MET cc_start: 0.7590 (mtp) cc_final: 0.7251 (mtp) REVERT: H 207 GLU cc_start: 0.6946 (tp30) cc_final: 0.6670 (tp30) REVERT: H 274 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8348 (mtp) outliers start: 21 outliers final: 16 residues processed: 253 average time/residue: 0.2816 time to fit residues: 113.2413 Evaluate side-chains 232 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU 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 149 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 156 LEU 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 274 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 176 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 67 ASN C 17 ASN C 279 ASN E 17 ASN E 53 ASN ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3865 r_free = 0.3865 target = 0.162824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122291 restraints weight = 33702.126| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.05 r_work: 0.3068 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20226 Z= 0.271 Angle : 0.686 11.738 27946 Z= 0.376 Chirality : 0.046 0.202 3197 Planarity : 0.005 0.045 3231 Dihedral : 18.160 179.843 3843 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.42 % Favored : 89.22 % Rotamer: Outliers : 2.12 % Allowed : 11.58 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.18), residues: 2218 helix: 0.71 (0.23), residues: 501 sheet: 0.57 (0.28), residues: 414 loop : -1.96 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 239 HIS 0.006 0.002 HIS D 225 PHE 0.042 0.003 PHE H 205 TYR 0.019 0.002 TYR G 252 ARG 0.005 0.001 ARG E 14 Details of bonding type rmsd hydrogen bonds : bond 0.05423 ( 620) hydrogen bonds : angle 4.51784 ( 1750) covalent geometry : bond 0.00634 (20226) covalent geometry : angle 0.68576 (27946) *********************** 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 268 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 2.084 Fit side-chains REVERT: A 7 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: A 174 GLU cc_start: 0.7675 (pp20) cc_final: 0.6834 (tm-30) REVERT: B 37 GLU cc_start: 0.7957 (tp30) cc_final: 0.7746 (tp30) REVERT: B 48 LYS cc_start: 0.7805 (mmmt) cc_final: 0.7213 (mtpp) REVERT: B 103 GLU cc_start: 0.5865 (tm-30) cc_final: 0.5492 (tm-30) REVERT: B 182 MET cc_start: 0.8105 (ttt) cc_final: 0.7826 (ttt) REVERT: B 219 MET cc_start: 0.7294 (tpt) cc_final: 0.6950 (tpt) REVERT: C 32 ASP cc_start: 0.7911 (m-30) cc_final: 0.7515 (p0) REVERT: C 42 LYS cc_start: 0.6165 (pttt) cc_final: 0.5667 (ttpt) REVERT: C 191 MET cc_start: 0.7570 (mtm) cc_final: 0.6917 (mtp) REVERT: C 294 ASN cc_start: 0.7703 (m-40) cc_final: 0.7406 (m-40) REVERT: D 210 LYS cc_start: 0.8189 (mttp) cc_final: 0.7952 (mmmt) REVERT: E 249 VAL cc_start: 0.9097 (m) cc_final: 0.8845 (m) REVERT: G 109 ASN cc_start: 0.8187 (t0) cc_final: 0.7760 (t0) REVERT: G 188 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8083 (mt-10) REVERT: H 172 MET cc_start: 0.7730 (mtp) cc_final: 0.7392 (mtp) REVERT: H 274 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8420 (mtp) outliers start: 39 outliers final: 31 residues processed: 254 average time/residue: 0.3426 time to fit residues: 138.8799 Evaluate side-chains 248 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 131 LEU 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 B residue 239 VAL 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 168 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 274 MET Chi-restraints excluded: chain H residue 289 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 182 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 190 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN E 294 ASN F 20 ASN 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 = 0.3910 r_free = 0.3910 target = 0.166965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126385 restraints weight = 35701.286| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.14 r_work: 0.3138 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20226 Z= 0.136 Angle : 0.570 9.474 27946 Z= 0.316 Chirality : 0.041 0.181 3197 Planarity : 0.004 0.041 3231 Dihedral : 18.062 176.995 3843 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.11 % Favored : 90.66 % Rotamer: Outliers : 2.61 % Allowed : 12.23 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2218 helix: 1.03 (0.23), residues: 500 sheet: 0.61 (0.28), residues: 414 loop : -1.88 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 130 HIS 0.003 0.001 HIS F 189 PHE 0.018 0.001 PHE B 202 TYR 0.019 0.001 TYR A 86 ARG 0.009 0.000 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 620) hydrogen bonds : angle 4.12196 ( 1750) covalent geometry : bond 0.00300 (20226) covalent geometry : angle 0.56967 (27946) *********************** 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 291 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 1.952 Fit side-chains REVERT: A 7 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: A 10 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.7834 (pt) REVERT: A 174 GLU cc_start: 0.7600 (pp20) cc_final: 0.6752 (tm-30) REVERT: B 37 GLU cc_start: 0.7865 (tp30) cc_final: 0.7606 (tp30) REVERT: B 48 LYS cc_start: 0.7707 (mmmt) cc_final: 0.7207 (mtpp) REVERT: B 103 GLU cc_start: 0.5743 (tm-30) cc_final: 0.5409 (tm-30) REVERT: B 151 VAL cc_start: 0.6898 (p) cc_final: 0.6675 (p) REVERT: B 182 MET cc_start: 0.8048 (ttt) cc_final: 0.7806 (ttt) REVERT: B 190 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: B 219 MET cc_start: 0.6962 (tpt) cc_final: 0.6672 (tpt) REVERT: C 32 ASP cc_start: 0.7921 (m-30) cc_final: 0.7533 (p0) REVERT: C 214 GLN cc_start: 0.6744 (pt0) cc_final: 0.6237 (pm20) REVERT: C 294 ASN cc_start: 0.7607 (m-40) cc_final: 0.7265 (m-40) REVERT: D 210 LYS cc_start: 0.8162 (mttp) cc_final: 0.7925 (mmmt) REVERT: E 289 MET cc_start: 0.8690 (mtm) cc_final: 0.8372 (mtp) REVERT: G 109 ASN cc_start: 0.8100 (t0) cc_final: 0.7630 (t0) REVERT: G 163 ASP cc_start: 0.7468 (t70) cc_final: 0.7221 (t70) REVERT: G 188 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8011 (mt-10) REVERT: G 191 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7041 (mpp) REVERT: H 172 MET cc_start: 0.7771 (mtp) cc_final: 0.7456 (mtp) REVERT: H 274 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8335 (mtp) outliers start: 48 outliers final: 32 residues processed: 275 average time/residue: 0.2781 time to fit residues: 121.4353 Evaluate side-chains 258 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 131 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 294 ASN Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 156 LEU 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 27 ASN 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 191 MET Chi-restraints excluded: chain G residue 247 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 183 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 178 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.0010 chunk 222 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN F 294 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 = 0.3913 r_free = 0.3913 target = 0.167262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125056 restraints weight = 35911.644| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.22 r_work: 0.3111 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20226 Z= 0.148 Angle : 0.570 9.531 27946 Z= 0.316 Chirality : 0.041 0.174 3197 Planarity : 0.004 0.041 3231 Dihedral : 17.997 177.879 3843 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.92 % Favored : 89.90 % Rotamer: Outliers : 2.83 % Allowed : 12.72 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.18), residues: 2218 helix: 1.08 (0.23), residues: 501 sheet: 0.59 (0.28), residues: 414 loop : -1.88 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 130 HIS 0.005 0.001 HIS E 72 PHE 0.019 0.001 PHE B 202 TYR 0.016 0.001 TYR A 86 ARG 0.006 0.000 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 620) hydrogen bonds : angle 4.05532 ( 1750) covalent geometry : bond 0.00334 (20226) covalent geometry : angle 0.57001 (27946) *********************** 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 284 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: A 10 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.7822 (pt) REVERT: A 174 GLU cc_start: 0.7580 (pp20) cc_final: 0.6770 (tm-30) REVERT: B 26 MET cc_start: 0.7921 (tpt) cc_final: 0.7660 (tpt) REVERT: B 37 GLU cc_start: 0.7841 (tp30) cc_final: 0.7549 (tp30) REVERT: B 48 LYS cc_start: 0.7717 (mmmt) cc_final: 0.7213 (mtpp) REVERT: B 103 GLU cc_start: 0.5820 (tm-30) cc_final: 0.5554 (tm-30) REVERT: B 151 VAL cc_start: 0.6951 (p) cc_final: 0.6716 (p) REVERT: B 182 MET cc_start: 0.8066 (ttt) cc_final: 0.7849 (ttt) REVERT: B 219 MET cc_start: 0.7035 (tpt) cc_final: 0.6799 (tpt) REVERT: C 32 ASP cc_start: 0.7914 (m-30) cc_final: 0.7545 (p0) REVERT: C 214 GLN cc_start: 0.6799 (pt0) cc_final: 0.6239 (pm20) REVERT: C 294 ASN cc_start: 0.7628 (m-40) cc_final: 0.7310 (m-40) REVERT: D 38 MET cc_start: 0.7956 (mmp) cc_final: 0.7753 (mmp) REVERT: D 210 LYS cc_start: 0.8170 (mttp) cc_final: 0.7926 (mmmt) REVERT: D 274 MET cc_start: 0.8255 (mtp) cc_final: 0.7872 (mtp) REVERT: E 289 MET cc_start: 0.8681 (mtm) cc_final: 0.8416 (mtp) REVERT: G 109 ASN cc_start: 0.8121 (t0) cc_final: 0.7640 (t0) REVERT: G 163 ASP cc_start: 0.7490 (t70) cc_final: 0.7207 (t70) REVERT: G 188 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8082 (mt-10) REVERT: G 191 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7297 (mpp) REVERT: H 172 MET cc_start: 0.7771 (mtp) cc_final: 0.7446 (mtp) REVERT: H 274 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8447 (mtp) outliers start: 52 outliers final: 44 residues processed: 268 average time/residue: 0.2836 time to fit residues: 120.8058 Evaluate side-chains 270 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 101 CYS 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 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 197 SER 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 156 LEU 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 5 LYS Chi-restraints excluded: chain G residue 27 ASN 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 114 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 MET 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 268 THR 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 226 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 184 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 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 = 0.3861 r_free = 0.3861 target = 0.162540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121990 restraints weight = 27166.258| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.49 r_work: 0.3108 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20226 Z= 0.230 Angle : 0.646 10.613 27946 Z= 0.356 Chirality : 0.044 0.183 3197 Planarity : 0.004 0.044 3231 Dihedral : 18.035 178.317 3843 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.60 % Favored : 89.08 % Rotamer: Outliers : 3.81 % Allowed : 12.40 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2218 helix: 0.85 (0.23), residues: 501 sheet: 0.31 (0.28), residues: 415 loop : -1.98 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 239 HIS 0.006 0.002 HIS D 225 PHE 0.027 0.002 PHE H 205 TYR 0.020 0.002 TYR A 86 ARG 0.009 0.001 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 620) hydrogen bonds : angle 4.30323 ( 1750) covalent geometry : bond 0.00534 (20226) covalent geometry : angle 0.64614 (27946) *********************** 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 288 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 1.878 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: A 10 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7690 (pt) REVERT: A 174 GLU cc_start: 0.7671 (pp20) cc_final: 0.6851 (tm-30) REVERT: B 37 GLU cc_start: 0.7887 (tp30) cc_final: 0.7619 (tp30) REVERT: B 48 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7475 (mtpp) REVERT: B 151 VAL cc_start: 0.6989 (p) cc_final: 0.6765 (p) REVERT: B 182 MET cc_start: 0.8070 (ttt) cc_final: 0.7850 (ttt) REVERT: C 32 ASP cc_start: 0.8028 (m-30) cc_final: 0.7670 (p0) REVERT: C 191 MET cc_start: 0.7391 (mtm) cc_final: 0.6732 (mtp) REVERT: C 294 ASN cc_start: 0.7761 (m-40) cc_final: 0.7471 (m-40) REVERT: D 210 LYS cc_start: 0.8161 (mttp) cc_final: 0.7958 (mmmt) REVERT: E 191 MET cc_start: 0.8236 (mtm) cc_final: 0.7994 (mtm) REVERT: E 289 MET cc_start: 0.8576 (mtm) cc_final: 0.8319 (mtp) REVERT: G 109 ASN cc_start: 0.8165 (t0) cc_final: 0.7701 (t0) REVERT: G 188 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7994 (mt-10) REVERT: G 191 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8042 (mtm) REVERT: G 207 GLU cc_start: 0.7463 (mp0) cc_final: 0.6660 (mm-30) REVERT: H 274 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8451 (mtp) REVERT: H 294 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8519 (t0) outliers start: 70 outliers final: 54 residues processed: 270 average time/residue: 0.2655 time to fit residues: 115.3322 Evaluate side-chains 272 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 101 CYS 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 168 GLU 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 86 VAL Chi-restraints excluded: chain D residue 107 LEU 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 197 SER Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 294 ASN 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 156 LEU Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 27 ASN 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 114 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 MET 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 268 THR 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 226 ASP 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 Chi-restraints excluded: chain H residue 294 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 11 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 136 optimal weight: 0.0870 chunk 162 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.168109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128142 restraints weight = 29533.457| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.41 r_work: 0.3202 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20226 Z= 0.124 Angle : 0.570 10.696 27946 Z= 0.313 Chirality : 0.041 0.180 3197 Planarity : 0.004 0.042 3231 Dihedral : 17.978 176.871 3843 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.38 % Favored : 90.44 % Rotamer: Outliers : 2.94 % Allowed : 13.81 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2218 helix: 1.12 (0.23), residues: 501 sheet: 0.52 (0.28), residues: 410 loop : -1.88 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 130 HIS 0.004 0.001 HIS E 72 PHE 0.023 0.001 PHE B 202 TYR 0.017 0.001 TYR G 240 ARG 0.009 0.000 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 620) hydrogen bonds : angle 3.99268 ( 1750) covalent geometry : bond 0.00269 (20226) covalent geometry : angle 0.57024 (27946) *********************** 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 289 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 235 time to evaluate : 2.073 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: A 10 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7784 (pt) REVERT: A 174 GLU cc_start: 0.7573 (pp20) cc_final: 0.6790 (tm-30) REVERT: B 37 GLU cc_start: 0.7850 (tp30) cc_final: 0.7571 (tp30) REVERT: B 48 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7387 (mtpp) REVERT: B 103 GLU cc_start: 0.5596 (tm-30) cc_final: 0.5293 (tm-30) REVERT: B 151 VAL cc_start: 0.6811 (p) cc_final: 0.6583 (p) REVERT: B 182 MET cc_start: 0.7924 (ttt) cc_final: 0.7696 (ttt) REVERT: B 198 MET cc_start: 0.8267 (mmm) cc_final: 0.8062 (mmm) REVERT: C 32 ASP cc_start: 0.8099 (m-30) cc_final: 0.7821 (p0) REVERT: C 191 MET cc_start: 0.7287 (mtm) cc_final: 0.6671 (mtp) REVERT: C 294 ASN cc_start: 0.7659 (m-40) cc_final: 0.7383 (m-40) REVERT: D 38 MET cc_start: 0.7865 (mmp) cc_final: 0.7543 (mmp) REVERT: E 191 MET cc_start: 0.8065 (mtm) cc_final: 0.7822 (mtm) REVERT: E 289 MET cc_start: 0.8575 (mtm) cc_final: 0.8302 (mtp) REVERT: G 109 ASN cc_start: 0.8058 (t0) cc_final: 0.7570 (t0) REVERT: G 188 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7924 (mt-10) REVERT: G 191 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7652 (mtm) REVERT: G 207 GLU cc_start: 0.7393 (mp0) cc_final: 0.6649 (mm-30) REVERT: H 172 MET cc_start: 0.7880 (mtp) cc_final: 0.7551 (mtp) REVERT: H 274 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8498 (mtp) REVERT: H 294 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8396 (t0) outliers start: 54 outliers final: 44 residues processed: 273 average time/residue: 0.2644 time to fit residues: 115.8116 Evaluate side-chains 278 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 101 CYS 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 168 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 252 TYR 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 156 LEU 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 5 LYS 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 191 MET 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 268 THR 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 226 ASP 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 294 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 74 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.165352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123747 restraints weight = 25253.558| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.38 r_work: 0.3115 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20226 Z= 0.185 Angle : 0.614 10.471 27946 Z= 0.336 Chirality : 0.042 0.250 3197 Planarity : 0.004 0.042 3231 Dihedral : 18.008 178.350 3843 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.33 % Favored : 89.45 % Rotamer: Outliers : 3.53 % Allowed : 13.76 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.18), residues: 2218 helix: 1.07 (0.23), residues: 502 sheet: 0.47 (0.28), residues: 410 loop : -1.92 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 130 HIS 0.005 0.001 HIS E 189 PHE 0.023 0.002 PHE B 202 TYR 0.021 0.002 TYR A 86 ARG 0.008 0.000 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 620) hydrogen bonds : angle 4.10075 ( 1750) covalent geometry : bond 0.00425 (20226) covalent geometry : angle 0.61421 (27946) *********************** 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 291 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 2.086 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: A 10 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7797 (pt) REVERT: A 174 GLU cc_start: 0.7592 (pp20) cc_final: 0.6801 (tm-30) REVERT: B 37 GLU cc_start: 0.7879 (tp30) cc_final: 0.7567 (tp30) REVERT: B 48 LYS cc_start: 0.7805 (mmmt) cc_final: 0.7230 (mtpp) REVERT: B 103 GLU cc_start: 0.5838 (tm-30) cc_final: 0.5554 (tm-30) REVERT: B 151 VAL cc_start: 0.6830 (p) cc_final: 0.6593 (p) REVERT: C 32 ASP cc_start: 0.8113 (m-30) cc_final: 0.7822 (p0) REVERT: C 191 MET cc_start: 0.7335 (mtm) cc_final: 0.6742 (mtp) REVERT: C 294 ASN cc_start: 0.7732 (m-40) cc_final: 0.7464 (m-40) REVERT: D 191 MET cc_start: 0.8034 (mpp) cc_final: 0.7596 (mmm) REVERT: E 191 MET cc_start: 0.8094 (mtm) cc_final: 0.7835 (mtm) REVERT: E 289 MET cc_start: 0.8529 (mtm) cc_final: 0.8268 (mtp) REVERT: G 109 ASN cc_start: 0.8126 (t0) cc_final: 0.7648 (t0) REVERT: G 163 ASP cc_start: 0.7739 (t70) cc_final: 0.7529 (t0) REVERT: G 188 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7962 (mt-10) REVERT: G 191 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7988 (mtm) REVERT: G 207 GLU cc_start: 0.7463 (mp0) cc_final: 0.6654 (mm-30) REVERT: H 172 MET cc_start: 0.7818 (mtp) cc_final: 0.7486 (mtp) REVERT: H 274 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8474 (mtp) REVERT: H 294 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8452 (t0) outliers start: 65 outliers final: 56 residues processed: 273 average time/residue: 0.2850 time to fit residues: 124.9343 Evaluate side-chains 283 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 222 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 131 LEU 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 101 CYS 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 168 GLU 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 86 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 129 LEU 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 197 SER Chi-restraints excluded: chain E residue 252 TYR 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 156 LEU Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 27 ASN 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 114 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 MET 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 268 THR 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 226 ASP 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 Chi-restraints excluded: chain H residue 294 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 222 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 135 optimal weight: 0.0770 chunk 174 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 61 optimal weight: 0.0570 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN E 214 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 = 0.3946 r_free = 0.3946 target = 0.170423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.128843 restraints weight = 33901.046| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.93 r_work: 0.3166 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 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 = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20226 Z= 0.113 Angle : 0.551 10.126 27946 Z= 0.302 Chirality : 0.040 0.217 3197 Planarity : 0.003 0.040 3231 Dihedral : 17.947 177.745 3843 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.84 % Favored : 90.98 % Rotamer: Outliers : 2.94 % Allowed : 14.41 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2218 helix: 1.37 (0.23), residues: 501 sheet: 0.31 (0.26), residues: 485 loop : -1.83 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 130 HIS 0.007 0.001 HIS H 225 PHE 0.023 0.001 PHE B 202 TYR 0.024 0.001 TYR A 86 ARG 0.007 0.000 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 620) hydrogen bonds : angle 3.81168 ( 1750) covalent geometry : bond 0.00234 (20226) covalent geometry : angle 0.55062 (27946) *********************** 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 295 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: A 10 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7710 (pt) REVERT: A 174 GLU cc_start: 0.7610 (pp20) cc_final: 0.6851 (tm-30) REVERT: B 7 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7179 (m) REVERT: B 37 GLU cc_start: 0.7640 (tp30) cc_final: 0.7322 (tp30) REVERT: B 48 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7176 (mtpp) REVERT: B 103 GLU cc_start: 0.5858 (tm-30) cc_final: 0.5533 (tm-30) REVERT: B 151 VAL cc_start: 0.6899 (p) cc_final: 0.6681 (p) REVERT: B 198 MET cc_start: 0.8323 (mmm) cc_final: 0.8013 (mmm) REVERT: C 32 ASP cc_start: 0.8102 (m-30) cc_final: 0.7820 (p0) REVERT: C 81 TYR cc_start: 0.7259 (p90) cc_final: 0.7042 (p90) REVERT: C 191 MET cc_start: 0.7283 (mtm) cc_final: 0.6766 (mtp) REVERT: C 294 ASN cc_start: 0.7636 (m-40) cc_final: 0.7370 (m-40) REVERT: D 191 MET cc_start: 0.7966 (mpp) cc_final: 0.7595 (mmm) REVERT: D 274 MET cc_start: 0.8093 (mtp) cc_final: 0.7892 (mtp) REVERT: E 191 MET cc_start: 0.8052 (mtm) cc_final: 0.7703 (mtm) REVERT: E 289 MET cc_start: 0.8617 (mtm) cc_final: 0.8344 (mtp) REVERT: F 108 GLU cc_start: 0.5460 (OUTLIER) cc_final: 0.3976 (mt-10) REVERT: G 109 ASN cc_start: 0.8094 (t0) cc_final: 0.7579 (t0) REVERT: G 188 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7978 (mt-10) REVERT: G 191 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7385 (mpp) REVERT: G 207 GLU cc_start: 0.7437 (mp0) cc_final: 0.6611 (mm-30) REVERT: H 172 MET cc_start: 0.7702 (mtp) cc_final: 0.7362 (mtp) REVERT: H 274 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8473 (mtp) outliers start: 54 outliers final: 40 residues processed: 281 average time/residue: 0.2752 time to fit residues: 123.8411 Evaluate side-chains 268 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 168 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 107 LEU 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 252 TYR 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 156 LEU 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 27 ASN 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 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 268 THR Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 59 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 141 optimal weight: 0.1980 chunk 223 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 191 optimal weight: 0.0170 chunk 47 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 overall best weight: 1.0420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN H 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126396 restraints weight = 29340.432| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.53 r_work: 0.3167 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20226 Z= 0.130 Angle : 0.569 10.166 27946 Z= 0.310 Chirality : 0.040 0.193 3197 Planarity : 0.003 0.041 3231 Dihedral : 17.926 179.157 3843 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.92 % Favored : 89.90 % Rotamer: Outliers : 2.56 % Allowed : 15.01 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2218 helix: 1.34 (0.23), residues: 501 sheet: 0.40 (0.26), residues: 470 loop : -1.82 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 130 HIS 0.004 0.001 HIS E 72 PHE 0.025 0.001 PHE B 202 TYR 0.024 0.001 TYR A 86 ARG 0.008 0.000 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 620) hydrogen bonds : angle 3.82839 ( 1750) covalent geometry : bond 0.00288 (20226) covalent geometry : angle 0.56910 (27946) ********************** 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 271 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 10 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7698 (pt) REVERT: A 174 GLU cc_start: 0.7540 (pp20) cc_final: 0.6789 (tm-30) REVERT: B 7 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7310 (m) REVERT: B 37 GLU cc_start: 0.7616 (tp30) cc_final: 0.7278 (tp30) REVERT: B 48 LYS cc_start: 0.7790 (mmmt) cc_final: 0.7185 (mtpp) REVERT: B 103 GLU cc_start: 0.5849 (tm-30) cc_final: 0.5535 (tm-30) REVERT: B 151 VAL cc_start: 0.6892 (p) cc_final: 0.6673 (p) REVERT: B 219 MET cc_start: 0.7005 (tpt) cc_final: 0.6675 (tpt) REVERT: B 227 ASP cc_start: 0.8200 (m-30) cc_final: 0.7984 (t0) REVERT: C 32 ASP cc_start: 0.8128 (m-30) cc_final: 0.7826 (p0) REVERT: C 191 MET cc_start: 0.7251 (mtm) cc_final: 0.6728 (mtp) REVERT: C 294 ASN cc_start: 0.7629 (m-40) cc_final: 0.7396 (m-40) REVERT: D 191 MET cc_start: 0.7918 (mpp) cc_final: 0.7471 (mmm) REVERT: E 191 MET cc_start: 0.7991 (mtm) cc_final: 0.7723 (mtm) REVERT: E 289 MET cc_start: 0.8588 (mtm) cc_final: 0.8315 (mtp) REVERT: F 108 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.3989 (mt-10) REVERT: G 109 ASN cc_start: 0.8062 (t0) cc_final: 0.7558 (t0) REVERT: G 188 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7963 (mt-10) REVERT: G 191 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7841 (mtm) REVERT: G 207 GLU cc_start: 0.7421 (mp0) cc_final: 0.6618 (mm-30) REVERT: H 172 MET cc_start: 0.7836 (mtp) cc_final: 0.7496 (mtp) REVERT: H 227 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: H 274 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8453 (mtp) outliers start: 47 outliers final: 39 residues processed: 258 average time/residue: 0.2778 time to fit residues: 115.4231 Evaluate side-chains 268 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 168 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 252 TYR 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 156 LEU Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 27 ASN 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 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 268 THR Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.164098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121126 restraints weight = 27909.614| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.54 r_work: 0.3071 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20226 Z= 0.227 Angle : 0.657 11.064 27946 Z= 0.357 Chirality : 0.044 0.178 3197 Planarity : 0.004 0.043 3231 Dihedral : 18.023 178.955 3843 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.65 % Favored : 89.08 % Rotamer: Outliers : 2.72 % Allowed : 15.01 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 2218 helix: 1.04 (0.23), residues: 502 sheet: 0.33 (0.28), residues: 414 loop : -1.92 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 239 HIS 0.006 0.002 HIS D 225 PHE 0.025 0.002 PHE B 202 TYR 0.021 0.002 TYR A 86 ARG 0.008 0.001 ARG F 133 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 620) hydrogen bonds : angle 4.18913 ( 1750) covalent geometry : bond 0.00524 (20226) covalent geometry : angle 0.65701 (27946) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11270.04 seconds wall clock time: 195 minutes 24.08 seconds (11724.08 seconds total)