Starting phenix.real_space_refine on Sun Aug 24 15:05:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyl_18757/08_2025/8qyl_18757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyl_18757/08_2025/8qyl_18757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qyl_18757/08_2025/8qyl_18757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyl_18757/08_2025/8qyl_18757.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyl_18757/08_2025/8qyl_18757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyl_18757/08_2025/8qyl_18757.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 131 5.16 5 C 13337 2.51 5 N 3571 2.21 5 O 3958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20997 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1791 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 220} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1916 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1880 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 233} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1760 Unusual residues: {'ACE': 1} Classifications: {'peptide': 229, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1898 Unusual residues: {'ACE': 1} Classifications: {'peptide': 241, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'ACE_C-N': 1, 'PTRANS': 10, 'TRANS': 230} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1876 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "G" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1892 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "H" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 777 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "I" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2128 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 253} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1956 Unusual residues: {'ACE': 1} Classifications: {'peptide': 249, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 15, 'TRANS': 233} Chain breaks: 2 Chain: "K" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1621 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1422 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain breaks: 2 Time building chain proxies: 4.59, per 1000 atoms: 0.22 Number of scatterers: 20997 At special positions: 0 Unit cell: (125.126, 142.15, 145.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 131 16.00 O 3958 8.00 N 3571 7.00 C 13337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 870.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5024 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 24 sheets defined 41.2% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.862A pdb=" N GLU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 102 removed outlier: 3.669A pdb=" N VAL A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.664A pdb=" N GLU A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.533A pdb=" N GLU B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.738A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.627A pdb=" N LEU B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 111 " --> pdb=" O CYS B 107 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.681A pdb=" N ALA B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 249 Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.614A pdb=" N GLU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.564A pdb=" N THR C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 59 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG C 60 " --> pdb=" O ARG C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 60' Processing helix chain 'C' and resid 76 through 98 removed outlier: 3.547A pdb=" N ALA C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 removed outlier: 3.943A pdb=" N TYR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 removed outlier: 4.106A pdb=" N VAL C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 221 through 241 removed outlier: 4.131A pdb=" N LYS C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 30 removed outlier: 3.549A pdb=" N GLU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 34 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 85 through 104 Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.830A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 185 Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 237 removed outlier: 3.702A pdb=" N VAL D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 26 removed outlier: 3.737A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 77 through 99 removed outlier: 3.710A pdb=" N ALA E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.971A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 176 through 179 removed outlier: 3.979A pdb=" N PHE E 179 " --> pdb=" O MET E 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 179' Processing helix chain 'E' and resid 183 through 196 Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'F' and resid 21 through 30 removed outlier: 3.616A pdb=" N GLU F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 34 removed outlier: 3.628A pdb=" N SER F 34 " --> pdb=" O VAL F 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 31 through 34' Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 122 removed outlier: 3.555A pdb=" N TYR F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 179 through 180 No H-bonds generated for 'chain 'F' and resid 179 through 180' Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.958A pdb=" N GLU F 184 " --> pdb=" O GLN F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 removed outlier: 4.319A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU F 193 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 229 through 244 Processing helix chain 'G' and resid 22 through 31 removed outlier: 3.556A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 35 removed outlier: 4.074A pdb=" N GLY G 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 32 through 35' Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 126 removed outlier: 3.650A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 3.528A pdb=" N SER G 175 " --> pdb=" O LYS G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 206 removed outlier: 3.678A pdb=" N VAL G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 Processing helix chain 'H' and resid 47 through 54 removed outlier: 4.301A pdb=" N SER H 51 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 71 Processing helix chain 'H' and resid 73 through 87 removed outlier: 3.684A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 107 Processing helix chain 'H' and resid 113 through 118 removed outlier: 3.844A pdb=" N ILE H 117 " --> pdb=" O GLY H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 138 Processing helix chain 'I' and resid 32 through 45 Processing helix chain 'I' and resid 61 through 66 removed outlier: 3.873A pdb=" N TYR I 66 " --> pdb=" O LEU I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 87 Processing helix chain 'I' and resid 142 through 154 removed outlier: 4.793A pdb=" N TYR I 147 " --> pdb=" O GLU I 143 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLN I 148 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'I' and resid 180 through 184 removed outlier: 3.866A pdb=" N LEU I 184 " --> pdb=" O THR I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 227 Processing helix chain 'I' and resid 243 through 249 Processing helix chain 'I' and resid 250 through 256 removed outlier: 3.550A pdb=" N SER I 255 " --> pdb=" O PRO I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 279 removed outlier: 3.586A pdb=" N SER I 269 " --> pdb=" O ASN I 265 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR I 279 " --> pdb=" O LYS I 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 66 through 70 removed outlier: 4.110A pdb=" N THR J 69 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU J 70 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 66 through 70' Processing helix chain 'J' and resid 98 through 114 removed outlier: 3.536A pdb=" N GLY J 114 " --> pdb=" O VAL J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 129 No H-bonds generated for 'chain 'J' and resid 127 through 129' Processing helix chain 'J' and resid 130 through 135 removed outlier: 3.599A pdb=" N ARG J 135 " --> pdb=" O ASP J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 159 removed outlier: 3.543A pdb=" N GLN J 152 " --> pdb=" O GLN J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 197 Processing helix chain 'J' and resid 213 through 229 removed outlier: 4.028A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 33 Processing helix chain 'K' and resid 92 through 114 Processing helix chain 'K' and resid 118 through 133 removed outlier: 3.547A pdb=" N ALA K 122 " --> pdb=" O ARG K 118 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR K 133 " --> pdb=" O MET K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 184 removed outlier: 3.764A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 207 removed outlier: 3.585A pdb=" N GLY K 205 " --> pdb=" O ALA K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 224 through 226 No H-bonds generated for 'chain 'K' and resid 224 through 226' Processing helix chain 'L' and resid 56 through 79 removed outlier: 3.650A pdb=" N GLN L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 98 removed outlier: 4.202A pdb=" N LYS L 98 " --> pdb=" O LEU L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 154 removed outlier: 4.389A pdb=" N MET L 149 " --> pdb=" O GLN L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 173 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.669A pdb=" N GLY A 43 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 69 removed outlier: 6.546A pdb=" N ILE A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 137 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.503A pdb=" N ILE B 37 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY B 42 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67 Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 62 through 66 removed outlier: 6.802A pdb=" N VAL C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 131 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 135 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 167 through 170 removed outlier: 3.652A pdb=" N GLU D 216 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 74 through 80 removed outlier: 3.805A pdb=" N GLY D 144 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 145 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU D 153 " --> pdb=" O CYS D 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB1, first strand: chain 'E' and resid 63 through 65 removed outlier: 3.586A pdb=" N LEU E 132 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 163 through 166 Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AB4, first strand: chain 'G' and resid 5 through 6 removed outlier: 6.079A pdb=" N SER G 5 " --> pdb=" O VAL I 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.130A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 69 through 71 Processing sheet with id=AB7, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.539A pdb=" N PHE I 123 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS I 98 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N CYS I 121 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL I 132 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS I 70 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N CYS I 135 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE I 72 " --> pdb=" O CYS I 135 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N CYS I 137 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA I 74 " --> pdb=" O CYS I 137 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS I 169 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 212 through 213 Processing sheet with id=AB9, first strand: chain 'J' and resid 1 through 4 removed outlier: 6.981A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR J 16 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU J 88 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU J 18 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU J 90 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU J 17 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU J 121 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET J 19 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL J 118 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU J 204 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL J 120 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LYS J 206 " --> pdb=" O VAL J 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 1 through 4 removed outlier: 6.981A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR J 16 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU J 88 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU J 18 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU J 90 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU J 17 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU J 121 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET J 19 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL J 118 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU J 204 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL J 120 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LYS J 206 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG J 140 " --> pdb=" O LEU J 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 41 through 42 removed outlier: 6.333A pdb=" N ILE K 84 " --> pdb=" O ILE K 80 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 41 through 42 Processing sheet with id=AC4, first strand: chain 'K' and resid 167 through 170 removed outlier: 3.516A pdb=" N GLY K 54 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 252 through 261 removed outlier: 6.598A pdb=" N THR L 199 " --> pdb=" O UNK K 255 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N UNK K 257 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR L 197 " --> pdb=" O UNK K 257 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N UNK K 259 " --> pdb=" O ILE L 195 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE L 195 " --> pdb=" O UNK K 259 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL L 185 " --> pdb=" O LEU L 200 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 42 through 44 1061 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3519 1.30 - 1.43: 5248 1.43 - 1.56: 12407 1.56 - 1.69: 0 1.69 - 1.82: 203 Bond restraints: 21377 Sorted by residual: bond pdb=" N VAL J 3 " pdb=" CA VAL J 3 " ideal model delta sigma weight residual 1.461 1.483 -0.023 9.10e-03 1.21e+04 6.30e+00 bond pdb=" N PHE D 2 " pdb=" CA PHE D 2 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.29e-02 6.01e+03 5.00e+00 bond pdb=" N ARG E 3 " pdb=" CA ARG E 3 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.32e-02 5.74e+03 4.49e+00 bond pdb=" N PHE E 2 " pdb=" CA PHE E 2 " ideal model delta sigma weight residual 1.456 1.478 -0.022 1.26e-02 6.30e+03 3.14e+00 bond pdb=" N PHE J 2 " pdb=" CA PHE J 2 " ideal model delta sigma weight residual 1.459 1.480 -0.020 1.24e-02 6.50e+03 2.65e+00 ... (remaining 21372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 28574 2.00 - 4.00: 273 4.00 - 5.99: 28 5.99 - 7.99: 2 7.99 - 9.99: 1 Bond angle restraints: 28878 Sorted by residual: angle pdb=" CA PHE E 2 " pdb=" CB PHE E 2 " pdb=" CG PHE E 2 " ideal model delta sigma weight residual 113.80 117.45 -3.65 1.00e+00 1.00e+00 1.34e+01 angle pdb=" N ARG E 3 " pdb=" CA ARG E 3 " pdb=" C ARG E 3 " ideal model delta sigma weight residual 113.17 108.77 4.40 1.26e+00 6.30e-01 1.22e+01 angle pdb=" C ACE D 0 " pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 121.70 131.69 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C ARG E 3 " pdb=" N ASN E 4 " pdb=" CA ASN E 4 " ideal model delta sigma weight residual 120.31 115.54 4.77 1.52e+00 4.33e-01 9.84e+00 angle pdb=" N GLU L 151 " pdb=" CA GLU L 151 " pdb=" CB GLU L 151 " ideal model delta sigma weight residual 110.12 114.67 -4.55 1.47e+00 4.63e-01 9.57e+00 ... (remaining 28873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 11821 17.89 - 35.78: 952 35.78 - 53.67: 136 53.67 - 71.57: 44 71.57 - 89.46: 21 Dihedral angle restraints: 12974 sinusoidal: 5176 harmonic: 7798 Sorted by residual: dihedral pdb=" CH3 ACE E 0 " pdb=" C ACE E 0 " pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sinusoidal sigma weight residual 180.00 -153.29 -26.71 1 5.00e+00 4.00e-02 4.10e+01 dihedral pdb=" CH3 ACE J 0 " pdb=" C ACE J 0 " pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sinusoidal sigma weight residual -180.00 -154.95 -25.05 1 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CH3 ACE D 0 " pdb=" C ACE D 0 " pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sinusoidal sigma weight residual -180.00 -160.33 -19.67 1 5.00e+00 4.00e-02 2.24e+01 ... (remaining 12971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2391 0.043 - 0.087: 643 0.087 - 0.130: 223 0.130 - 0.173: 13 0.173 - 0.217: 2 Chirality restraints: 3272 Sorted by residual: chirality pdb=" CA VAL J 3 " pdb=" N VAL J 3 " pdb=" C VAL J 3 " pdb=" CB VAL J 3 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR D 113 " pdb=" CA THR D 113 " pdb=" OG1 THR D 113 " pdb=" CG2 THR D 113 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA GLN I 208 " pdb=" N GLN I 208 " pdb=" C GLN I 208 " pdb=" CB GLN I 208 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 3269 not shown) Planarity restraints: 3698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE J 0 " 0.042 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" O ACE J 0 " 0.023 2.00e-02 2.50e+03 pdb=" CH3 ACE J 0 " -0.117 2.00e-02 2.50e+03 pdb=" N MET J 1 " 0.207 2.00e-02 2.50e+03 pdb=" CA MET J 1 " -0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE E 0 " -0.034 2.00e-02 2.50e+03 1.23e-01 1.91e+02 pdb=" O ACE E 0 " -0.011 2.00e-02 2.50e+03 pdb=" CH3 ACE E 0 " 0.106 2.00e-02 2.50e+03 pdb=" N MET E 1 " -0.206 2.00e-02 2.50e+03 pdb=" CA MET E 1 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE D 0 " 0.021 2.00e-02 2.50e+03 8.77e-02 9.62e+01 pdb=" O ACE D 0 " 0.007 2.00e-02 2.50e+03 pdb=" CH3 ACE D 0 " -0.074 2.00e-02 2.50e+03 pdb=" N MET D 1 " 0.149 2.00e-02 2.50e+03 pdb=" CA MET D 1 " -0.102 2.00e-02 2.50e+03 ... (remaining 3695 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3054 2.76 - 3.30: 18261 3.30 - 3.83: 32284 3.83 - 4.37: 38546 4.37 - 4.90: 70238 Nonbonded interactions: 162383 Sorted by model distance: nonbonded pdb=" NH1 ARG A 143 " pdb=" O PRO A 144 " model vdw 2.225 3.120 nonbonded pdb=" NH1 ARG A 84 " pdb=" OD1 ASP G 120 " model vdw 2.247 3.120 nonbonded pdb=" OD2 ASP F 203 " pdb=" NZ LYS F 206 " model vdw 2.257 3.120 nonbonded pdb=" OG1 THR G 67 " pdb=" OE2 GLU G 216 " model vdw 2.265 3.040 nonbonded pdb=" O UNK K 249 " pdb=" NE2 GLN L 169 " model vdw 2.269 3.120 ... (remaining 162378 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.270 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21377 Z= 0.146 Angle : 0.519 9.989 28878 Z= 0.280 Chirality : 0.044 0.217 3272 Planarity : 0.006 0.129 3698 Dihedral : 13.753 89.457 7950 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.16), residues: 2629 helix: 2.30 (0.17), residues: 951 sheet: 0.50 (0.21), residues: 541 loop : -0.84 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 60 TYR 0.013 0.001 TYR B 136 PHE 0.020 0.001 PHE L 69 TRP 0.067 0.002 TRP F 216 HIS 0.004 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00337 (21377) covalent geometry : angle 0.51916 (28878) hydrogen bonds : bond 0.17577 ( 1046) hydrogen bonds : angle 5.97080 ( 3048) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.861 Fit side-chains REVERT: C 102 VAL cc_start: 0.8636 (t) cc_final: 0.8413 (p) REVERT: J 96 LYS cc_start: 0.7716 (mmpt) cc_final: 0.7443 (mmmt) REVERT: L 142 CYS cc_start: 0.6943 (t) cc_final: 0.5989 (t) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.7667 time to fit residues: 251.8257 Evaluate side-chains 242 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.0050 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 ASN B 177 GLN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN G 53 GLN G 100 ASN G 147 GLN H 108 ASN I 103 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.078384 restraints weight = 30739.798| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.46 r_work: 0.2814 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21377 Z= 0.255 Angle : 0.641 8.109 28878 Z= 0.343 Chirality : 0.048 0.194 3272 Planarity : 0.006 0.065 3698 Dihedral : 4.720 36.589 2913 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.23 % Allowed : 8.89 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.16), residues: 2629 helix: 2.15 (0.17), residues: 958 sheet: 0.66 (0.21), residues: 560 loop : -1.03 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 188 TYR 0.022 0.002 TYR B 136 PHE 0.026 0.002 PHE K 79 TRP 0.038 0.002 TRP F 216 HIS 0.008 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00645 (21377) covalent geometry : angle 0.64082 (28878) hydrogen bonds : bond 0.07425 ( 1046) hydrogen bonds : angle 4.56594 ( 3048) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.882 Fit side-chains REVERT: A 215 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: B 230 GLN cc_start: 0.7330 (mm-40) cc_final: 0.7079 (tt0) REVERT: F 181 GLN cc_start: 0.7926 (pp30) cc_final: 0.7670 (pp30) REVERT: G 59 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8039 (ttpt) REVERT: G 184 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6854 (mtmt) REVERT: I 103 ASN cc_start: 0.7223 (m110) cc_final: 0.7006 (m-40) REVERT: L 142 CYS cc_start: 0.6588 (t) cc_final: 0.6340 (t) REVERT: L 191 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7864 (mt-10) outliers start: 28 outliers final: 11 residues processed: 266 average time/residue: 0.8435 time to fit residues: 247.8599 Evaluate side-chains 255 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 221 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN B 177 GLN D 214 ASN G 147 GLN H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN J 229 GLN L 61 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.080184 restraints weight = 30790.386| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.47 r_work: 0.2844 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21377 Z= 0.162 Angle : 0.542 7.622 28878 Z= 0.292 Chirality : 0.044 0.167 3272 Planarity : 0.005 0.055 3698 Dihedral : 4.516 36.513 2913 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.85 % Allowed : 11.09 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.16), residues: 2629 helix: 2.29 (0.17), residues: 962 sheet: 0.78 (0.21), residues: 566 loop : -0.97 (0.17), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 3 TYR 0.015 0.001 TYR B 136 PHE 0.023 0.001 PHE K 79 TRP 0.020 0.001 TRP F 216 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00396 (21377) covalent geometry : angle 0.54212 (28878) hydrogen bonds : bond 0.05708 ( 1046) hydrogen bonds : angle 4.27080 ( 3048) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 249 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: B 230 GLN cc_start: 0.7250 (mm-40) cc_final: 0.6994 (tt0) REVERT: E 51 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6521 (mpt-90) REVERT: E 217 LYS cc_start: 0.8149 (pmtt) cc_final: 0.7788 (tttp) REVERT: F 181 GLN cc_start: 0.8159 (pp30) cc_final: 0.7886 (pp30) REVERT: F 233 ARG cc_start: 0.7690 (mtm110) cc_final: 0.7348 (mtp85) REVERT: G 184 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6666 (mtmt) REVERT: H 129 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.5494 (tm-30) REVERT: K 26 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7075 (mt-10) REVERT: L 142 CYS cc_start: 0.6729 (t) cc_final: 0.6513 (t) REVERT: L 146 MET cc_start: 0.7826 (mpt) cc_final: 0.7568 (mpt) REVERT: L 155 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: L 191 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7969 (mt-10) outliers start: 42 outliers final: 16 residues processed: 268 average time/residue: 0.8663 time to fit residues: 256.3348 Evaluate side-chains 257 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 191 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 247 optimal weight: 40.0000 chunk 50 optimal weight: 9.9990 chunk 245 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 262 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN D 214 ASN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN H 108 ASN I 161 ASN I 163 GLN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.078610 restraints weight = 30846.755| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.43 r_work: 0.2798 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21377 Z= 0.213 Angle : 0.593 8.794 28878 Z= 0.316 Chirality : 0.046 0.181 3272 Planarity : 0.006 0.054 3698 Dihedral : 4.650 37.413 2913 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.51 % Allowed : 12.32 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.16), residues: 2629 helix: 2.20 (0.17), residues: 967 sheet: 0.76 (0.21), residues: 570 loop : -1.05 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 188 TYR 0.019 0.002 TYR B 136 PHE 0.027 0.002 PHE K 79 TRP 0.015 0.002 TRP F 216 HIS 0.006 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00536 (21377) covalent geometry : angle 0.59252 (28878) hydrogen bonds : bond 0.06642 ( 1046) hydrogen bonds : angle 4.30042 ( 3048) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 244 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: B 230 GLN cc_start: 0.7319 (mm-40) cc_final: 0.7054 (tt0) REVERT: D 191 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5847 (tt) REVERT: E 51 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6896 (mpt-90) REVERT: E 203 GLN cc_start: 0.6723 (mp10) cc_final: 0.6475 (mp10) REVERT: E 217 LYS cc_start: 0.8181 (pmtt) cc_final: 0.7806 (tttp) REVERT: F 181 GLN cc_start: 0.8221 (pp30) cc_final: 0.7995 (pp30) REVERT: G 59 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8023 (ttpt) REVERT: G 184 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6763 (mtmt) REVERT: H 129 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.5613 (tm-30) REVERT: I 88 MET cc_start: 0.8259 (mtm) cc_final: 0.8022 (mmm) REVERT: K 26 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7204 (mt-10) REVERT: L 142 CYS cc_start: 0.6750 (t) cc_final: 0.6479 (t) REVERT: L 146 MET cc_start: 0.7907 (mpt) cc_final: 0.7636 (mpt) REVERT: L 155 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: L 191 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8026 (mt-10) outliers start: 57 outliers final: 23 residues processed: 274 average time/residue: 0.8378 time to fit residues: 254.5015 Evaluate side-chains 271 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain L residue 149 MET Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 78 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 193 optimal weight: 0.0980 chunk 20 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN D 214 ASN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.080828 restraints weight = 30516.494| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.43 r_work: 0.2874 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21377 Z= 0.135 Angle : 0.514 7.507 28878 Z= 0.277 Chirality : 0.043 0.161 3272 Planarity : 0.005 0.051 3698 Dihedral : 4.421 35.958 2913 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.29 % Allowed : 13.24 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.16), residues: 2629 helix: 2.39 (0.17), residues: 969 sheet: 0.84 (0.21), residues: 565 loop : -0.95 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 3 TYR 0.015 0.001 TYR F 239 PHE 0.021 0.001 PHE K 79 TRP 0.011 0.001 TRP F 216 HIS 0.004 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00321 (21377) covalent geometry : angle 0.51398 (28878) hydrogen bonds : bond 0.05080 ( 1046) hydrogen bonds : angle 4.10555 ( 3048) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: B 230 GLN cc_start: 0.7324 (mm-40) cc_final: 0.7063 (tt0) REVERT: C 102 VAL cc_start: 0.8686 (t) cc_final: 0.8371 (p) REVERT: D 114 GLN cc_start: 0.7017 (tm-30) cc_final: 0.6544 (tm-30) REVERT: D 191 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5787 (tt) REVERT: D 224 GLN cc_start: 0.6079 (pm20) cc_final: 0.5765 (pm20) REVERT: E 51 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6814 (mpt-90) REVERT: E 203 GLN cc_start: 0.6567 (mp10) cc_final: 0.6341 (mp10) REVERT: G 59 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8030 (ttpt) REVERT: G 184 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6586 (mtmt) REVERT: H 61 LYS cc_start: 0.7174 (mtmt) cc_final: 0.6967 (mtmt) REVERT: H 129 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.5551 (tm-30) REVERT: I 88 MET cc_start: 0.8343 (mtm) cc_final: 0.8108 (mmm) REVERT: I 101 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8207 (pp) REVERT: I 280 ASN cc_start: 0.6008 (OUTLIER) cc_final: 0.5662 (m-40) REVERT: K 26 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7064 (mt-10) REVERT: L 142 CYS cc_start: 0.6939 (t) cc_final: 0.6339 (t) REVERT: L 146 MET cc_start: 0.7864 (mpt) cc_final: 0.7511 (mpt) REVERT: L 191 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7997 (mt-10) outliers start: 52 outliers final: 25 residues processed: 277 average time/residue: 0.8355 time to fit residues: 256.3486 Evaluate side-chains 273 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain L residue 149 MET Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 23 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 210 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 123 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN D 214 ASN F 181 GLN G 147 GLN H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN L 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.081937 restraints weight = 30576.703| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.44 r_work: 0.2892 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21377 Z= 0.114 Angle : 0.494 8.205 28878 Z= 0.265 Chirality : 0.042 0.170 3272 Planarity : 0.005 0.049 3698 Dihedral : 4.256 34.942 2913 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.33 % Allowed : 13.81 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.16), residues: 2629 helix: 2.49 (0.17), residues: 972 sheet: 0.90 (0.21), residues: 563 loop : -0.89 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 3 TYR 0.015 0.001 TYR F 239 PHE 0.019 0.001 PHE K 79 TRP 0.009 0.001 TRP D 100 HIS 0.004 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00263 (21377) covalent geometry : angle 0.49396 (28878) hydrogen bonds : bond 0.04480 ( 1046) hydrogen bonds : angle 3.99200 ( 3048) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: B 230 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6953 (tt0) REVERT: C 102 VAL cc_start: 0.8623 (t) cc_final: 0.8312 (p) REVERT: D 114 GLN cc_start: 0.6951 (tm-30) cc_final: 0.6445 (tm-30) REVERT: D 191 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5717 (tt) REVERT: D 210 LEU cc_start: 0.7631 (mp) cc_final: 0.6976 (mt) REVERT: E 51 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6728 (mpt-90) REVERT: F 72 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7166 (ptm160) REVERT: F 181 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7616 (pp30) REVERT: H 61 LYS cc_start: 0.7064 (mtmt) cc_final: 0.6852 (mtmt) REVERT: H 129 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.5291 (tm-30) REVERT: I 88 MET cc_start: 0.8304 (mtm) cc_final: 0.8074 (mmm) REVERT: I 280 ASN cc_start: 0.5932 (OUTLIER) cc_final: 0.5628 (m-40) REVERT: I 281 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5843 (pp20) REVERT: K 26 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7095 (mt-10) REVERT: L 142 CYS cc_start: 0.7019 (t) cc_final: 0.6673 (t) REVERT: L 146 MET cc_start: 0.7825 (mpt) cc_final: 0.7562 (mpt) REVERT: L 191 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7968 (mt-10) outliers start: 53 outliers final: 21 residues processed: 280 average time/residue: 0.8397 time to fit residues: 260.3445 Evaluate side-chains 271 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 149 MET Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 211 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 111 optimal weight: 0.0060 chunk 86 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 146 GLN B 177 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN G 147 GLN H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.084361 restraints weight = 30641.626| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.44 r_work: 0.2934 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21377 Z= 0.092 Angle : 0.469 6.840 28878 Z= 0.251 Chirality : 0.041 0.148 3272 Planarity : 0.004 0.046 3698 Dihedral : 4.033 32.641 2913 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.80 % Allowed : 14.61 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.16), residues: 2629 helix: 2.65 (0.17), residues: 972 sheet: 0.99 (0.21), residues: 560 loop : -0.76 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 60 TYR 0.014 0.001 TYR K 133 PHE 0.017 0.001 PHE K 79 TRP 0.009 0.001 TRP D 100 HIS 0.003 0.000 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00197 (21377) covalent geometry : angle 0.46881 (28878) hydrogen bonds : bond 0.03558 ( 1046) hydrogen bonds : angle 3.85216 ( 3048) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 230 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6950 (tt0) REVERT: D 114 GLN cc_start: 0.7048 (tm-30) cc_final: 0.6554 (tm-30) REVERT: D 191 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5648 (tt) REVERT: E 51 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6739 (mpt-90) REVERT: E 234 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8107 (pm20) REVERT: F 72 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7137 (ptm160) REVERT: H 61 LYS cc_start: 0.7109 (mtmt) cc_final: 0.6880 (mtmt) REVERT: I 88 MET cc_start: 0.8384 (mtm) cc_final: 0.8170 (mmm) REVERT: I 281 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5797 (pp20) REVERT: K 26 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7230 (mt-10) REVERT: K 107 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: L 142 CYS cc_start: 0.7049 (t) cc_final: 0.6701 (t) REVERT: L 146 MET cc_start: 0.7786 (mpt) cc_final: 0.7520 (mpt) REVERT: L 191 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7988 (mt-10) outliers start: 41 outliers final: 17 residues processed: 271 average time/residue: 0.8446 time to fit residues: 253.4293 Evaluate side-chains 268 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain K residue 107 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 35 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 247 optimal weight: 40.0000 chunk 0 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN B 177 GLN D 214 ASN F 181 GLN G 147 GLN H 56 GLN H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.082462 restraints weight = 30532.497| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.44 r_work: 0.2868 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21377 Z= 0.119 Angle : 0.503 9.401 28878 Z= 0.268 Chirality : 0.042 0.182 3272 Planarity : 0.005 0.048 3698 Dihedral : 4.103 32.738 2913 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.89 % Allowed : 15.31 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.16), residues: 2629 helix: 2.63 (0.17), residues: 972 sheet: 0.92 (0.21), residues: 582 loop : -0.72 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 60 TYR 0.016 0.001 TYR K 133 PHE 0.021 0.001 PHE K 79 TRP 0.009 0.001 TRP D 100 HIS 0.004 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00279 (21377) covalent geometry : angle 0.50260 (28878) hydrogen bonds : bond 0.04454 ( 1046) hydrogen bonds : angle 3.90569 ( 3048) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: B 230 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6947 (tt0) REVERT: D 114 GLN cc_start: 0.7069 (tm-30) cc_final: 0.6560 (tm-30) REVERT: D 191 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5770 (tt) REVERT: D 210 LEU cc_start: 0.7647 (mp) cc_final: 0.7058 (mt) REVERT: E 51 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6733 (mpt-90) REVERT: E 203 GLN cc_start: 0.6649 (mp10) cc_final: 0.6280 (mp10) REVERT: E 234 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: F 72 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7183 (ptm160) REVERT: G 3 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7986 (mmm-85) REVERT: H 61 LYS cc_start: 0.7108 (mtmt) cc_final: 0.6866 (mtmt) REVERT: H 62 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6900 (ptt) REVERT: H 129 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.5248 (tm-30) REVERT: I 88 MET cc_start: 0.8255 (mtm) cc_final: 0.8042 (mmm) REVERT: I 101 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8165 (pp) REVERT: I 280 ASN cc_start: 0.6059 (OUTLIER) cc_final: 0.5789 (m-40) REVERT: I 281 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5882 (pp20) REVERT: K 107 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: L 142 CYS cc_start: 0.7012 (t) cc_final: 0.6710 (t) REVERT: L 146 MET cc_start: 0.7862 (mpt) cc_final: 0.7600 (mpt) REVERT: L 173 ASN cc_start: 0.8686 (t0) cc_final: 0.8282 (p0) REVERT: L 191 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8029 (mt-10) outliers start: 43 outliers final: 23 residues processed: 269 average time/residue: 0.8412 time to fit residues: 250.8418 Evaluate side-chains 280 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 78 optimal weight: 7.9990 chunk 221 optimal weight: 0.0770 chunk 192 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 177 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN G 53 GLN G 147 GLN H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.078932 restraints weight = 30579.906| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.42 r_work: 0.2805 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21377 Z= 0.215 Angle : 0.606 10.675 28878 Z= 0.321 Chirality : 0.046 0.245 3272 Planarity : 0.005 0.052 3698 Dihedral : 4.493 35.478 2913 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.16 % Allowed : 14.87 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.16), residues: 2629 helix: 2.38 (0.17), residues: 969 sheet: 0.88 (0.21), residues: 575 loop : -0.90 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 186 TYR 0.019 0.002 TYR B 136 PHE 0.029 0.002 PHE K 79 TRP 0.010 0.002 TRP G 101 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00539 (21377) covalent geometry : angle 0.60607 (28878) hydrogen bonds : bond 0.06473 ( 1046) hydrogen bonds : angle 4.17123 ( 3048) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: B 230 GLN cc_start: 0.7269 (mm-40) cc_final: 0.7002 (tt0) REVERT: D 114 GLN cc_start: 0.7117 (tm-30) cc_final: 0.6600 (tm-30) REVERT: D 191 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5863 (tt) REVERT: D 210 LEU cc_start: 0.7692 (mp) cc_final: 0.6976 (mt) REVERT: D 211 ASN cc_start: 0.8077 (m110) cc_final: 0.7767 (t0) REVERT: E 51 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6788 (mpt-90) REVERT: E 203 GLN cc_start: 0.6788 (mp10) cc_final: 0.6451 (mp10) REVERT: E 234 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: F 72 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7267 (ptm160) REVERT: H 62 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6939 (ptt) REVERT: H 129 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.5561 (tm-30) REVERT: I 88 MET cc_start: 0.8254 (mtm) cc_final: 0.8039 (mmm) REVERT: I 101 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8215 (pp) REVERT: I 177 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8219 (p) REVERT: I 281 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5901 (pp20) REVERT: J 149 LYS cc_start: 0.7936 (mmpt) cc_final: 0.7429 (mmmt) REVERT: K 26 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7354 (mt-10) REVERT: L 142 CYS cc_start: 0.6808 (t) cc_final: 0.6425 (t) REVERT: L 146 MET cc_start: 0.7826 (mpt) cc_final: 0.7536 (mpt) REVERT: L 149 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6966 (mtp) REVERT: L 173 ASN cc_start: 0.8709 (t0) cc_final: 0.8113 (p0) REVERT: L 191 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7953 (mt-10) outliers start: 49 outliers final: 26 residues processed: 277 average time/residue: 0.8107 time to fit residues: 249.3546 Evaluate side-chains 280 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain L residue 149 MET Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 194 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN G 53 GLN G 147 GLN H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.079705 restraints weight = 30775.753| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.43 r_work: 0.2811 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21377 Z= 0.183 Angle : 0.574 10.222 28878 Z= 0.306 Chirality : 0.045 0.189 3272 Planarity : 0.005 0.052 3698 Dihedral : 4.487 37.303 2913 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.85 % Allowed : 15.31 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.16), residues: 2629 helix: 2.36 (0.17), residues: 968 sheet: 0.86 (0.21), residues: 575 loop : -0.92 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 186 TYR 0.018 0.001 TYR F 239 PHE 0.025 0.002 PHE K 79 TRP 0.009 0.001 TRP D 100 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00457 (21377) covalent geometry : angle 0.57381 (28878) hydrogen bonds : bond 0.05836 ( 1046) hydrogen bonds : angle 4.13361 ( 3048) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: B 230 GLN cc_start: 0.7294 (mm-40) cc_final: 0.7037 (tt0) REVERT: D 114 GLN cc_start: 0.7089 (tm-30) cc_final: 0.6596 (tm-30) REVERT: D 191 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5856 (tt) REVERT: D 210 LEU cc_start: 0.7697 (mp) cc_final: 0.6973 (mt) REVERT: D 211 ASN cc_start: 0.8095 (m110) cc_final: 0.7782 (t0) REVERT: E 51 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6730 (mpt-90) REVERT: E 203 GLN cc_start: 0.6678 (mp10) cc_final: 0.6390 (mp10) REVERT: E 234 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: F 72 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7261 (ptm160) REVERT: H 129 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.5519 (tm-30) REVERT: I 88 MET cc_start: 0.8236 (mtm) cc_final: 0.8032 (mmm) REVERT: I 101 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8184 (pp) REVERT: I 177 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8201 (p) REVERT: I 280 ASN cc_start: 0.5829 (OUTLIER) cc_final: 0.5531 (m-40) REVERT: I 281 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5960 (pp20) REVERT: J 149 LYS cc_start: 0.7933 (mmpt) cc_final: 0.7412 (mmmt) REVERT: K 26 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7285 (mt-10) REVERT: L 142 CYS cc_start: 0.6818 (t) cc_final: 0.6395 (t) REVERT: L 146 MET cc_start: 0.7794 (mpt) cc_final: 0.7484 (mpt) REVERT: L 191 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7923 (mt-10) outliers start: 42 outliers final: 28 residues processed: 267 average time/residue: 0.7284 time to fit residues: 215.8441 Evaluate side-chains 280 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 241 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 239 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN G 53 GLN G 147 GLN H 108 ASN I 161 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.079783 restraints weight = 30760.670| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.45 r_work: 0.2844 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.281 21377 Z= 0.227 Angle : 0.822 59.195 28878 Z= 0.446 Chirality : 0.053 1.697 3272 Planarity : 0.006 0.196 3698 Dihedral : 4.484 37.109 2913 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.89 % Allowed : 15.44 % Favored : 82.67 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.16), residues: 2629 helix: 2.36 (0.17), residues: 969 sheet: 0.85 (0.21), residues: 575 loop : -0.93 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 186 TYR 0.017 0.001 TYR B 136 PHE 0.025 0.002 PHE K 79 TRP 0.009 0.001 TRP D 100 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00504 (21377) covalent geometry : angle 0.82235 (28878) hydrogen bonds : bond 0.05713 ( 1046) hydrogen bonds : angle 4.13271 ( 3048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8755.08 seconds wall clock time: 149 minutes 38.00 seconds (8978.00 seconds total)