Starting phenix.real_space_refine on Wed Jun 18 05:41:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyl_18757/06_2025/8qyl_18757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyl_18757/06_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_18757/06_2025/8qyl_18757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyl_18757/06_2025/8qyl_18757.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyl_18757/06_2025/8qyl_18757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyl_18757/06_2025/8qyl_18757.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3} 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: {'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 1, 'GLU:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 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: 12.25, per 1000 atoms: 0.58 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: 5.12 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 2.43 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: 7.06 Time building geometry restraints manager: 6.09 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: 1.800 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: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.110 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.610 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (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 TRP 0.067 0.002 TRP F 216 HIS 0.004 0.001 HIS D 73 PHE 0.020 0.001 PHE L 69 TYR 0.013 0.001 TYR B 136 ARG 0.005 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.17577 ( 1046) hydrogen bonds : angle 5.97080 ( 3048) covalent geometry : bond 0.00337 (21377) covalent geometry : angle 0.51916 (28878) *********************** 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 : 2.264 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: 1.6437 time to fit residues: 542.4368 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 : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 135 optimal weight: 0.2980 chunk 107 optimal weight: 0.8980 chunk 208 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 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 = 0.3595 r_free = 0.3595 target = 0.122726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.080778 restraints weight = 30539.252| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.46 r_work: 0.2851 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21377 Z= 0.164 Angle : 0.555 8.551 28878 Z= 0.299 Chirality : 0.044 0.164 3272 Planarity : 0.005 0.053 3698 Dihedral : 4.426 33.397 2913 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.23 % Allowed : 8.01 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2629 helix: 2.34 (0.17), residues: 962 sheet: 0.83 (0.21), residues: 549 loop : -0.93 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 216 HIS 0.006 0.001 HIS I 125 PHE 0.023 0.001 PHE K 79 TYR 0.017 0.001 TYR B 136 ARG 0.010 0.000 ARG F 188 Details of bonding type rmsd hydrogen bonds : bond 0.05907 ( 1046) hydrogen bonds : angle 4.45170 ( 3048) covalent geometry : bond 0.00396 (21377) covalent geometry : angle 0.55500 (28878) *********************** 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 286 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 2.414 Fit side-chains REVERT: A 215 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7981 (pm20) REVERT: B 230 GLN cc_start: 0.7319 (mm-40) cc_final: 0.7064 (tt0) REVERT: C 102 VAL cc_start: 0.8708 (t) cc_final: 0.8379 (p) REVERT: F 100 ARG cc_start: 0.8283 (tpp80) cc_final: 0.8061 (ttm-80) REVERT: F 181 GLN cc_start: 0.7843 (pp30) cc_final: 0.7564 (pp30) REVERT: G 59 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8028 (ttpt) REVERT: G 184 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6825 (mtmt) REVERT: H 80 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: H 109 ASP cc_start: 0.8056 (p0) cc_final: 0.7839 (p0) REVERT: J 96 LYS cc_start: 0.7481 (mmpt) cc_final: 0.7261 (mmpt) REVERT: J 229 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8542 (tp-100) REVERT: K 26 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7195 (mt-10) REVERT: K 32 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.5599 (ttm-80) REVERT: L 142 CYS cc_start: 0.6629 (t) cc_final: 0.6395 (t) REVERT: L 191 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7818 (mt-10) outliers start: 28 outliers final: 7 residues processed: 269 average time/residue: 1.5764 time to fit residues: 472.6644 Evaluate side-chains 255 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 241 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 200 THR 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 H residue 80 GLN Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain K residue 32 ARG 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 21 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 12 optimal weight: 0.0670 chunk 191 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 260 optimal weight: 0.8980 chunk 210 optimal weight: 10.0000 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 123 GLN B 146 GLN B 177 GLN ** D 73 HIS ** 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 L 61 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.125236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.083638 restraints weight = 30418.061| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.48 r_work: 0.2886 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21377 Z= 0.100 Angle : 0.468 7.210 28878 Z= 0.253 Chirality : 0.042 0.143 3272 Planarity : 0.004 0.048 3698 Dihedral : 4.117 31.052 2913 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.72 % Allowed : 9.72 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.16), residues: 2629 helix: 2.59 (0.17), residues: 962 sheet: 1.02 (0.21), residues: 545 loop : -0.81 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 216 HIS 0.004 0.001 HIS E 65 PHE 0.018 0.001 PHE K 79 TYR 0.013 0.001 TYR F 239 ARG 0.007 0.000 ARG F 188 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 1046) hydrogen bonds : angle 4.09109 ( 3048) covalent geometry : bond 0.00219 (21377) covalent geometry : angle 0.46843 (28878) *********************** 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 296 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 257 time to evaluate : 2.274 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: B 230 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6938 (tt0) REVERT: D 191 LEU cc_start: 0.5973 (OUTLIER) cc_final: 0.5754 (tt) REVERT: E 217 LYS cc_start: 0.8140 (pmtt) cc_final: 0.7792 (tttp) REVERT: F 72 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7214 (ptm160) REVERT: F 100 ARG cc_start: 0.8094 (tpp80) cc_final: 0.7844 (ttm-80) REVERT: F 181 GLN cc_start: 0.8085 (pp30) cc_final: 0.7827 (pp30) REVERT: H 62 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6800 (ptt) REVERT: H 129 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.5183 (tm-30) REVERT: J 96 LYS cc_start: 0.7348 (mmpt) cc_final: 0.7126 (mmpt) REVERT: J 229 GLN cc_start: 0.8733 (tp40) cc_final: 0.8525 (tp-100) REVERT: K 26 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7210 (mt-10) REVERT: L 155 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: L 171 MET cc_start: 0.7278 (tpt) cc_final: 0.6815 (tpt) REVERT: L 191 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7856 (mt-10) outliers start: 39 outliers final: 11 residues processed: 273 average time/residue: 1.5968 time to fit residues: 484.5308 Evaluate side-chains 263 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 77 THR 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 205 VAL 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 231 ASP Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain L residue 135 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 145 optimal weight: 8.9990 chunk 194 optimal weight: 0.8980 chunk 254 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 120 optimal weight: 0.2980 chunk 164 optimal weight: 0.0870 chunk 40 optimal weight: 3.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 78 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.086466 restraints weight = 30673.122| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.49 r_work: 0.2935 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21377 Z= 0.085 Angle : 0.439 7.423 28878 Z= 0.235 Chirality : 0.040 0.135 3272 Planarity : 0.004 0.047 3698 Dihedral : 3.827 26.620 2913 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.58 % Allowed : 11.31 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.17), residues: 2629 helix: 2.69 (0.17), residues: 974 sheet: 1.07 (0.21), residues: 554 loop : -0.65 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 216 HIS 0.003 0.000 HIS D 186 PHE 0.017 0.001 PHE K 79 TYR 0.013 0.001 TYR F 239 ARG 0.007 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 1046) hydrogen bonds : angle 3.82672 ( 3048) covalent geometry : bond 0.00177 (21377) covalent geometry : angle 0.43854 (28878) *********************** 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 299 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 263 time to evaluate : 2.430 Fit side-chains revert: symmetry clash REVERT: A 202 GLN cc_start: 0.8545 (tp40) cc_final: 0.8016 (tp40) REVERT: B 230 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6872 (tt0) REVERT: D 114 GLN cc_start: 0.6804 (tm-30) cc_final: 0.6384 (tm-30) REVERT: D 191 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.5452 (tt) REVERT: E 182 CYS cc_start: 0.7012 (m) cc_final: 0.6804 (m) REVERT: E 217 LYS cc_start: 0.8165 (pmtt) cc_final: 0.7781 (tttp) REVERT: F 72 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7107 (ptm160) REVERT: F 181 GLN cc_start: 0.8210 (pp30) cc_final: 0.7984 (pp30) REVERT: F 233 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7195 (mtp85) REVERT: I 151 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: I 281 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5115 (pm20) REVERT: J 229 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8534 (tp-100) REVERT: K 26 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7201 (mt-10) REVERT: K 107 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: K 147 ASP cc_start: 0.7487 (p0) cc_final: 0.7278 (p0) REVERT: L 171 MET cc_start: 0.7360 (tpt) cc_final: 0.6828 (tpt) REVERT: L 191 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7883 (mt-10) outliers start: 36 outliers final: 9 residues processed: 276 average time/residue: 1.6338 time to fit residues: 502.1066 Evaluate side-chains 266 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL 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 185 ASN Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 135 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 204 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 167 ASN B 177 GLN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN D 221 GLN D 224 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.120236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.078442 restraints weight = 30894.946| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.43 r_work: 0.2827 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 21377 Z= 0.264 Angle : 0.630 9.541 28878 Z= 0.333 Chirality : 0.048 0.188 3272 Planarity : 0.006 0.061 3698 Dihedral : 4.513 34.921 2913 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.20 % Allowed : 11.97 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.16), residues: 2629 helix: 2.35 (0.17), residues: 968 sheet: 0.94 (0.21), residues: 570 loop : -0.89 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 216 HIS 0.006 0.001 HIS I 125 PHE 0.029 0.002 PHE K 79 TYR 0.023 0.002 TYR B 136 ARG 0.006 0.001 ARG L 26 Details of bonding type rmsd hydrogen bonds : bond 0.07130 ( 1046) hydrogen bonds : angle 4.25852 ( 3048) covalent geometry : bond 0.00670 (21377) covalent geometry : angle 0.63009 (28878) *********************** 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 290 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 2.580 Fit side-chains revert: symmetry clash REVERT: B 230 GLN cc_start: 0.7348 (mm-40) cc_final: 0.7084 (tt0) REVERT: D 107 MET cc_start: 0.7372 (ttm) cc_final: 0.6998 (mtm) REVERT: D 114 GLN cc_start: 0.7034 (tm-30) cc_final: 0.6575 (tm-30) REVERT: D 191 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5888 (tt) REVERT: E 51 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6887 (mpt-90) REVERT: F 72 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7291 (ptm160) REVERT: H 129 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.5656 (tm-30) REVERT: I 88 MET cc_start: 0.8294 (mtm) cc_final: 0.8060 (mmm) REVERT: I 120 PHE cc_start: 0.6933 (p90) cc_final: 0.6732 (p90) REVERT: I 151 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: J 229 GLN cc_start: 0.8900 (tp40) cc_final: 0.8646 (tp-100) REVERT: K 26 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7162 (mt-10) REVERT: L 155 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: L 191 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8027 (mt-10) outliers start: 50 outliers final: 21 residues processed: 266 average time/residue: 1.5929 time to fit residues: 472.2653 Evaluate side-chains 257 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 102 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 D residue 224 GLN Chi-restraints excluded: chain D residue 228 MET 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 72 ARG 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 H residue 129 GLU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 179 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 155 GLU 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 75 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 259 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.080852 restraints weight = 30646.516| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.44 r_work: 0.2847 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21377 Z= 0.140 Angle : 0.522 8.121 28878 Z= 0.280 Chirality : 0.043 0.166 3272 Planarity : 0.005 0.051 3698 Dihedral : 4.338 34.194 2913 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.89 % Allowed : 13.29 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.16), residues: 2629 helix: 2.47 (0.17), residues: 971 sheet: 1.03 (0.21), residues: 554 loop : -0.89 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 216 HIS 0.004 0.001 HIS E 65 PHE 0.021 0.001 PHE K 79 TYR 0.016 0.001 TYR F 239 ARG 0.008 0.000 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.05148 ( 1046) hydrogen bonds : angle 4.07453 ( 3048) covalent geometry : bond 0.00335 (21377) covalent geometry : angle 0.52228 (28878) *********************** 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 279 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 2.406 Fit side-chains revert: symmetry clash REVERT: B 230 GLN cc_start: 0.7288 (mm-40) cc_final: 0.7039 (tt0) REVERT: D 107 MET cc_start: 0.7349 (ttm) cc_final: 0.7000 (mtm) REVERT: D 114 GLN cc_start: 0.6918 (tm-30) cc_final: 0.6457 (tm-30) REVERT: D 191 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5767 (tt) REVERT: D 210 LEU cc_start: 0.7625 (mp) cc_final: 0.6892 (mt) REVERT: E 51 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6836 (mpt-90) REVERT: E 234 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8109 (pm20) REVERT: F 72 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7234 (ptm160) REVERT: F 181 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7543 (pp30) REVERT: H 61 LYS cc_start: 0.7101 (mtmt) cc_final: 0.6893 (mtmt) REVERT: H 129 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.5465 (tm-30) REVERT: I 88 MET cc_start: 0.8292 (mtm) cc_final: 0.8069 (mmm) REVERT: I 151 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: I 280 ASN cc_start: 0.5965 (OUTLIER) cc_final: 0.5637 (m-40) REVERT: I 281 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5792 (pp20) REVERT: J 229 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8588 (tp-100) REVERT: K 107 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: L 155 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: L 191 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7884 (mt-10) outliers start: 43 outliers final: 19 residues processed: 262 average time/residue: 1.5829 time to fit residues: 461.5985 Evaluate side-chains 265 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 2.428 ------------------------------------------------------------------------------- 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 B residue 200 THR 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 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 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 H residue 129 GLU Chi-restraints excluded: chain I residue 151 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 229 GLN 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 135 ASP Chi-restraints excluded: chain L residue 155 GLU 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 8 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 111 optimal weight: 0.0020 chunk 261 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 chunk 208 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- 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 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** 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 = 0.3612 r_free = 0.3612 target = 0.123960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.082671 restraints weight = 30550.012| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.44 r_work: 0.2877 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21377 Z= 0.104 Angle : 0.482 6.989 28878 Z= 0.259 Chirality : 0.042 0.162 3272 Planarity : 0.005 0.049 3698 Dihedral : 4.134 32.389 2913 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.02 % Allowed : 13.29 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.16), residues: 2629 helix: 2.59 (0.17), residues: 973 sheet: 1.04 (0.21), residues: 562 loop : -0.79 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 100 HIS 0.004 0.001 HIS E 65 PHE 0.019 0.001 PHE K 79 TYR 0.016 0.001 TYR F 239 ARG 0.009 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 1046) hydrogen bonds : angle 3.94580 ( 3048) covalent geometry : bond 0.00232 (21377) covalent geometry : angle 0.48239 (28878) *********************** 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 288 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 2.291 Fit side-chains revert: symmetry clash REVERT: B 230 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6943 (tt0) REVERT: D 107 MET cc_start: 0.7354 (ttm) cc_final: 0.7045 (mtm) REVERT: D 114 GLN cc_start: 0.6891 (tm-30) cc_final: 0.6418 (tm-30) REVERT: D 191 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5611 (tt) REVERT: D 210 LEU cc_start: 0.7628 (mp) cc_final: 0.6900 (mt) REVERT: E 51 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6970 (mpt-90) REVERT: E 234 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8087 (pm20) REVERT: F 72 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7197 (ptm160) REVERT: H 61 LYS cc_start: 0.6987 (mtmt) cc_final: 0.6770 (mtmt) REVERT: H 129 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.5252 (tm-30) REVERT: I 88 MET cc_start: 0.8213 (mtm) cc_final: 0.7999 (mmm) REVERT: I 151 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: I 280 ASN cc_start: 0.6006 (OUTLIER) cc_final: 0.5698 (m-40) REVERT: I 281 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5748 (pp20) REVERT: J 229 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8531 (tp-100) REVERT: K 26 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7352 (mt-10) REVERT: K 107 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: L 191 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7865 (mt-10) outliers start: 46 outliers final: 19 residues processed: 272 average time/residue: 1.5691 time to fit residues: 479.2128 Evaluate side-chains 263 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 102 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 10 VAL Chi-restraints excluded: chain E residue 51 ARG 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 90 GLN Chi-restraints excluded: chain G residue 108 GLU 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 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 229 GLN Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 191 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 246 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 260 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 41 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 H 56 GLN H 108 ASN I 161 ASN I 163 GLN ** 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 = 0.3581 r_free = 0.3581 target = 0.121433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.079559 restraints weight = 30526.953| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.48 r_work: 0.2830 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21377 Z= 0.202 Angle : 0.580 9.543 28878 Z= 0.309 Chirality : 0.045 0.192 3272 Planarity : 0.005 0.051 3698 Dihedral : 4.425 34.758 2913 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.07 % Allowed : 13.77 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 2629 helix: 2.41 (0.17), residues: 969 sheet: 0.91 (0.21), residues: 570 loop : -0.89 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 100 HIS 0.005 0.001 HIS I 125 PHE 0.026 0.002 PHE K 79 TYR 0.019 0.002 TYR B 136 ARG 0.009 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.06155 ( 1046) hydrogen bonds : angle 4.13336 ( 3048) covalent geometry : bond 0.00505 (21377) covalent geometry : angle 0.58006 (28878) *********************** 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 283 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 2.412 Fit side-chains revert: symmetry clash REVERT: B 230 GLN cc_start: 0.7276 (mm-40) cc_final: 0.7017 (tt0) REVERT: D 114 GLN cc_start: 0.6947 (tm-30) cc_final: 0.6449 (tm-30) REVERT: D 191 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5794 (tt) REVERT: D 211 ASN cc_start: 0.8071 (m110) cc_final: 0.7791 (t0) REVERT: E 51 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7002 (mpt-90) REVERT: E 234 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: F 72 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7263 (ptm160) REVERT: G 59 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7996 (ttpt) REVERT: H 61 LYS cc_start: 0.7057 (mtmt) cc_final: 0.6847 (mtmt) REVERT: H 129 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.5451 (tm-30) REVERT: I 88 MET cc_start: 0.8193 (mtm) cc_final: 0.7983 (mmm) REVERT: I 151 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: I 280 ASN cc_start: 0.5913 (OUTLIER) cc_final: 0.5610 (m-40) REVERT: I 281 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5872 (pp20) REVERT: J 149 LYS cc_start: 0.8043 (mmpt) cc_final: 0.7455 (mmmt) REVERT: J 229 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8569 (tp-100) REVERT: K 26 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7309 (mt-10) REVERT: K 107 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: L 191 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7902 (mt-10) outliers start: 47 outliers final: 21 residues processed: 266 average time/residue: 1.5799 time to fit residues: 467.8662 Evaluate side-chains 266 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 2.520 ------------------------------------------------------------------------------- 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 102 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 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 201 VAL 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 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 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 229 GLN 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 135 ASP 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 233 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 211 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** D 41 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.079073 restraints weight = 30804.784| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.45 r_work: 0.2808 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1315 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= 0.214 Angle : 0.603 9.109 28878 Z= 0.320 Chirality : 0.046 0.226 3272 Planarity : 0.006 0.054 3698 Dihedral : 4.537 36.635 2913 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.16 % Allowed : 13.86 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2629 helix: 2.31 (0.17), residues: 969 sheet: 0.89 (0.21), residues: 570 loop : -0.99 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 100 HIS 0.005 0.001 HIS I 125 PHE 0.027 0.002 PHE K 79 TYR 0.020 0.002 TYR B 136 ARG 0.009 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.06373 ( 1046) hydrogen bonds : angle 4.18269 ( 3048) covalent geometry : bond 0.00538 (21377) covalent geometry : angle 0.60295 (28878) *********************** 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 287 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 2.516 Fit side-chains revert: symmetry clash REVERT: B 230 GLN cc_start: 0.7292 (mm-40) cc_final: 0.7041 (tt0) REVERT: D 114 GLN cc_start: 0.6955 (tm-30) cc_final: 0.6474 (tm-30) REVERT: D 191 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5842 (tt) REVERT: D 210 LEU cc_start: 0.7656 (mp) cc_final: 0.7011 (mt) REVERT: D 211 ASN cc_start: 0.8090 (m110) cc_final: 0.7793 (t0) REVERT: E 51 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6984 (mpt-90) REVERT: E 234 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: F 72 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7311 (ptm160) REVERT: G 59 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7984 (ttpt) REVERT: H 129 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.5506 (tm-30) REVERT: I 88 MET cc_start: 0.8208 (mtm) cc_final: 0.8002 (mmm) REVERT: I 151 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: I 280 ASN cc_start: 0.5860 (OUTLIER) cc_final: 0.5558 (m-40) REVERT: I 281 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5887 (pp20) REVERT: J 229 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8551 (tp-100) REVERT: K 26 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7331 (mt-10) REVERT: K 107 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: L 191 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8024 (mt-10) outliers start: 49 outliers final: 22 residues processed: 267 average time/residue: 1.5107 time to fit residues: 450.4297 Evaluate side-chains 269 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 2.286 ------------------------------------------------------------------------------- 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 B residue 200 THR Chi-restraints excluded: chain C residue 102 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 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 59 LYS Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU 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 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 229 GLN 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 135 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 146 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 180 optimal weight: 0.0870 chunk 256 optimal weight: 5.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.083429 restraints weight = 30328.525| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.47 r_work: 0.2907 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 21377 Z= 0.106 Angle : 0.497 10.087 28878 Z= 0.267 Chirality : 0.042 0.174 3272 Planarity : 0.005 0.050 3698 Dihedral : 4.171 33.604 2913 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.36 % Allowed : 14.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.16), residues: 2629 helix: 2.58 (0.17), residues: 972 sheet: 1.04 (0.21), residues: 561 loop : -0.86 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 149 HIS 0.004 0.001 HIS E 65 PHE 0.019 0.001 PHE K 79 TYR 0.016 0.001 TYR F 239 ARG 0.008 0.000 ARG F 233 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 1046) hydrogen bonds : angle 3.91658 ( 3048) covalent geometry : bond 0.00238 (21377) covalent geometry : angle 0.49699 (28878) ********************** 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 269 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 2.442 Fit side-chains revert: symmetry clash REVERT: B 230 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6966 (tt0) REVERT: D 114 GLN cc_start: 0.7012 (tm-30) cc_final: 0.6511 (tm-30) REVERT: D 191 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5703 (tt) REVERT: D 210 LEU cc_start: 0.7692 (mp) cc_final: 0.6939 (mt) REVERT: D 211 ASN cc_start: 0.8016 (m110) cc_final: 0.7760 (t0) REVERT: E 51 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7089 (mpt-90) REVERT: E 234 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: F 72 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7195 (ptm160) REVERT: H 129 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.5239 (tm-30) REVERT: I 151 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: I 281 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5759 (pp20) REVERT: J 149 LYS cc_start: 0.7871 (mmpt) cc_final: 0.7370 (mmmt) REVERT: J 229 GLN cc_start: 0.8764 (tp40) cc_final: 0.8504 (tp-100) REVERT: K 26 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7315 (mt-10) REVERT: K 107 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: L 191 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7909 (mt-10) outliers start: 31 outliers final: 19 residues processed: 259 average time/residue: 1.6115 time to fit residues: 468.9870 Evaluate side-chains 259 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 2.318 ------------------------------------------------------------------------------- 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 102 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 191 LEU Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 108 GLU 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 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 K residue 107 GLU Chi-restraints excluded: chain L residue 135 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.2335 > 50: distance: 53 - 58: 5.969 distance: 58 - 59: 3.612 distance: 59 - 60: 9.060 distance: 59 - 62: 3.929 distance: 60 - 61: 6.849 distance: 60 - 69: 12.809 distance: 62 - 63: 6.203 distance: 63 - 64: 5.172 distance: 63 - 65: 10.971 distance: 64 - 66: 12.951 distance: 65 - 67: 9.986 distance: 66 - 68: 10.059 distance: 67 - 68: 3.037 distance: 69 - 70: 14.051 distance: 70 - 71: 9.407 distance: 70 - 73: 9.869 distance: 71 - 72: 21.636 distance: 71 - 75: 19.621 distance: 73 - 74: 4.836 distance: 75 - 76: 26.334 distance: 75 - 81: 5.418 distance: 76 - 77: 26.017 distance: 76 - 79: 10.430 distance: 77 - 82: 25.143 distance: 79 - 80: 20.186 distance: 80 - 81: 23.556 distance: 82 - 83: 30.086 distance: 83 - 84: 21.025 distance: 83 - 86: 19.710 distance: 84 - 85: 17.034 distance: 84 - 91: 23.677 distance: 86 - 87: 9.238 distance: 87 - 88: 17.339 distance: 88 - 89: 10.343 distance: 88 - 90: 17.320 distance: 91 - 92: 4.127 distance: 92 - 93: 12.858 distance: 93 - 94: 9.118 distance: 93 - 95: 8.811 distance: 95 - 96: 14.125 distance: 96 - 97: 7.403 distance: 96 - 99: 6.067 distance: 97 - 106: 4.816 distance: 99 - 100: 9.724 distance: 100 - 101: 10.244 distance: 101 - 102: 7.648 distance: 103 - 105: 6.072 distance: 107 - 108: 4.628 distance: 108 - 109: 3.350 distance: 108 - 114: 6.099 distance: 110 - 111: 6.550 distance: 111 - 112: 13.071 distance: 111 - 113: 14.663 distance: 116 - 117: 7.524 distance: 116 - 126: 3.998 distance: 117 - 151: 8.605 distance: 119 - 121: 4.158 distance: 120 - 122: 3.159 distance: 123 - 124: 4.834 distance: 127 - 128: 4.318 distance: 127 - 130: 4.126 distance: 128 - 129: 3.377 distance: 128 - 135: 3.426 distance: 129 - 163: 6.046 distance: 130 - 131: 6.780 distance: 132 - 133: 5.584 distance: 132 - 134: 4.267 distance: 135 - 136: 4.258 distance: 136 - 139: 4.111 distance: 137 - 138: 5.316 distance: 137 - 142: 4.984 distance: 138 - 168: 11.854 distance: 139 - 140: 5.864 distance: 139 - 141: 5.278