Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:26:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y26_33586/12_2022/7y26_33586.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y26_33586/12_2022/7y26_33586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y26_33586/12_2022/7y26_33586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y26_33586/12_2022/7y26_33586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y26_33586/12_2022/7y26_33586.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y26_33586/12_2022/7y26_33586.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.007 sd= 0.154 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 130": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "E GLU 251": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8014 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2420 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 8, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1687 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 4, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 8, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Classifications: {'peptide': 8} Modifications used: {'COO': 1, 'PEPT-D': 2} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'DPN%PEPT-D:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1633 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 212} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1881 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 127 Chain: "F" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 327 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 5.15, per 1000 atoms: 0.64 Number of scatterers: 8014 At special positions: 0 Unit cell: (92.02, 128.14, 129.86, 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 53 16.00 O 1489 8.00 N 1355 7.00 C 5117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.32 Conformation dependent library (CDL) restraints added in 1.3 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN C 1 " pdb=" CB DTR C 4 " Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.7% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 Processing helix chain 'A' and resid 29 through 35 removed outlier: 3.578A pdb=" N ILE A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.942A pdb=" N ASN B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.916A pdb=" N ASP B 91 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.690A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 4.291A pdb=" N ARG B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 removed outlier: 4.210A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 202 " --> pdb=" O VAL B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.812A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.879A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.794A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'E' and resid 42 through 71 Processing helix chain 'E' and resid 77 through 93 removed outlier: 3.858A pdb=" N TYR E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET E 93 " --> pdb=" O ASP E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 112 through 146 removed outlier: 4.022A pdb=" N ARG E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE E 127 " --> pdb=" O GLY E 123 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA E 143 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 removed outlier: 3.872A pdb=" N LYS E 152 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 175 removed outlier: 3.636A pdb=" N THR E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA E 165 " --> pdb=" O MET E 161 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL E 166 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP E 167 " --> pdb=" O THR E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 203 through 238 removed outlier: 5.486A pdb=" N VAL E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) Proline residue: E 220 - end of helix removed outlier: 3.893A pdb=" N CYS E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR E 228 " --> pdb=" O ILE E 224 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 282 Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 287 through 301 removed outlier: 3.665A pdb=" N LYS E 291 " --> pdb=" O THR E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.783A pdb=" N CYS E 306 " --> pdb=" O TYR E 302 " (cutoff:3.500A) Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 319 through 326 removed outlier: 3.693A pdb=" N VAL E 326 " --> pdb=" O SER E 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 removed outlier: 3.608A pdb=" N ASN F 24 " --> pdb=" O LYS F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 44 removed outlier: 3.614A pdb=" N HIS F 44 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 48 removed outlier: 3.827A pdb=" N ASP F 48 " --> pdb=" O ALA F 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.645A pdb=" N ARG A 49 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS A 317 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 63 removed outlier: 3.538A pdb=" N TYR A 59 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA A 73 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N MET A 61 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL A 71 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP A 63 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU A 69 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 74 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS A 91 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP A 83 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS A 89 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105 removed outlier: 3.633A pdb=" N THR A 102 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 115 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY A 116 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN A 125 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL A 135 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 153 removed outlier: 7.053A pdb=" N SER A 160 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS A 149 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 158 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N PHE A 151 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLN A 156 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 161 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 178 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 removed outlier: 3.913A pdb=" N SER A 189 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 202 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN A 220 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ASP A 212 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS A 218 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 234 removed outlier: 7.029A pdb=" N GLY A 244 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A 232 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA A 242 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE A 234 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA A 240 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET A 262 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP A 254 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLU A 260 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 273 through 278 removed outlier: 4.087A pdb=" N SER A 275 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY A 306 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP A 298 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG A 304 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 76 removed outlier: 3.724A pdb=" N PHE B 70 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP B 85 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 212 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 143 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.650A pdb=" N ARG D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.163A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 98 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 135 removed outlier: 3.571A pdb=" N THR D 231 " --> pdb=" O TYR D 215 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR D 163 " --> pdb=" O MET D 218 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE D 177 " --> pdb=" O TRP D 164 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 178 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D 182 " --> pdb=" O TYR D 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 182 through 185 removed outlier: 3.604A pdb=" N GLY E 182 " --> pdb=" O THR E 194 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1155 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: 2.39 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2595 1.34 - 1.46: 2021 1.46 - 1.58: 3492 1.58 - 1.70: 0 1.70 - 1.81: 74 Bond restraints: 8182 Sorted by residual: bond pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.51e+00 bond pdb=" C VAL D 64 " pdb=" O VAL D 64 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.10e-01 bond pdb=" CA GLU A 130 " pdb=" CB GLU A 130 " ideal model delta sigma weight residual 1.532 1.545 -0.013 1.51e-02 4.39e+03 6.93e-01 bond pdb=" C ALA A 287 " pdb=" N GLY A 288 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.39e-02 5.18e+03 6.52e-01 bond pdb=" CG1 ILE E 174 " pdb=" CD1 ILE E 174 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.54e-01 ... (remaining 8177 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.93: 178 106.93 - 113.72: 4571 113.72 - 120.50: 3078 120.50 - 127.28: 3265 127.28 - 134.06: 86 Bond angle restraints: 11178 Sorted by residual: angle pdb=" CA GLU A 130 " pdb=" CB GLU A 130 " pdb=" CG GLU A 130 " ideal model delta sigma weight residual 114.10 120.43 -6.33 2.00e+00 2.50e-01 1.00e+01 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.57e+00 angle pdb=" C ILE E 174 " pdb=" CA ILE E 174 " pdb=" CB ILE E 174 " ideal model delta sigma weight residual 111.29 106.80 4.49 1.64e+00 3.72e-01 7.49e+00 angle pdb=" CA MET D 180 " pdb=" CB MET D 180 " pdb=" CG MET D 180 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.72e+00 angle pdb=" C GLY D 197 " pdb=" N THR D 198 " pdb=" CA THR D 198 " ideal model delta sigma weight residual 122.40 126.07 -3.67 1.45e+00 4.76e-01 6.41e+00 ... (remaining 11173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4372 17.98 - 35.96: 295 35.96 - 53.94: 55 53.94 - 71.92: 6 71.92 - 89.90: 2 Dihedral angle restraints: 4730 sinusoidal: 1512 harmonic: 3218 Sorted by residual: dihedral pdb=" CB CYS E 115 " pdb=" SG CYS E 115 " pdb=" SG CYS E 193 " pdb=" CB CYS E 193 " ideal model delta sinusoidal sigma weight residual -86.00 -175.90 89.90 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS D 147 " pdb=" SG CYS D 147 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 -178.60 -88.40 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CA THR D 160 " pdb=" C THR D 160 " pdb=" N TYR D 161 " pdb=" CA TYR D 161 " ideal model delta harmonic sigma weight residual -180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 858 0.032 - 0.065: 305 0.065 - 0.097: 107 0.097 - 0.129: 50 0.129 - 0.161: 7 Chirality restraints: 1327 Sorted by residual: chirality pdb=" CB VAL E 106 " pdb=" CA VAL E 106 " pdb=" CG1 VAL E 106 " pdb=" CG2 VAL E 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA MET D 180 " pdb=" N MET D 180 " pdb=" C MET D 180 " pdb=" CB MET D 180 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA ILE D 58 " pdb=" N ILE D 58 " pdb=" C ILE D 58 " pdb=" CB ILE D 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1324 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 48 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO F 49 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO F 49 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 49 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 214 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C ILE E 214 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE E 214 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU E 215 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 74 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO D 75 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.021 5.00e-02 4.00e+02 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 707 2.74 - 3.28: 7563 3.28 - 3.82: 12108 3.82 - 4.36: 12622 4.36 - 4.90: 24172 Nonbonded interactions: 57172 Sorted by model distance: nonbonded pdb=" O LEU D 153 " pdb=" OG1 THR D 160 " model vdw 2.203 2.440 nonbonded pdb=" NH2 ARG D 67 " pdb=" OD2 ASP D 90 " model vdw 2.297 2.520 nonbonded pdb=" NZ LYS D 151 " pdb=" O SER D 152 " model vdw 2.299 2.520 nonbonded pdb=" O GLY A 224 " pdb=" NH1 ARG A 251 " model vdw 2.308 2.520 nonbonded pdb=" O TYR B 170 " pdb=" NH2 ARG B 188 " model vdw 2.326 2.520 ... (remaining 57167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5117 2.51 5 N 1355 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.460 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.080 Process input model: 25.210 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 0.031 8182 Z= 0.199 Angle : 0.565 6.332 11178 Z= 0.315 Chirality : 0.042 0.161 1327 Planarity : 0.004 0.043 1418 Dihedral : 12.616 70.709 2641 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.25), residues: 1081 helix: 2.36 (0.27), residues: 372 sheet: 0.86 (0.32), residues: 254 loop : -1.50 (0.26), residues: 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.956 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1745 time to fit residues: 35.1330 Evaluate side-chains 117 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 244 ASN D 159 ASN E 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8182 Z= 0.134 Angle : 0.485 5.738 11178 Z= 0.261 Chirality : 0.041 0.149 1327 Planarity : 0.003 0.036 1418 Dihedral : 3.885 27.970 1180 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1081 helix: 2.53 (0.27), residues: 376 sheet: 0.95 (0.33), residues: 263 loop : -1.30 (0.28), residues: 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 0.990 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 133 average time/residue: 0.1884 time to fit residues: 34.6006 Evaluate side-chains 116 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0723 time to fit residues: 2.0685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 8182 Z= 0.381 Angle : 0.645 7.244 11178 Z= 0.352 Chirality : 0.046 0.150 1327 Planarity : 0.004 0.042 1418 Dihedral : 4.608 25.281 1180 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.26), residues: 1081 helix: 2.12 (0.27), residues: 368 sheet: 0.48 (0.32), residues: 264 loop : -1.47 (0.27), residues: 449 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.006 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 124 average time/residue: 0.1525 time to fit residues: 26.8897 Evaluate side-chains 111 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0760 time to fit residues: 1.8564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS E 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8182 Z= 0.232 Angle : 0.556 6.621 11178 Z= 0.302 Chirality : 0.043 0.154 1327 Planarity : 0.004 0.041 1418 Dihedral : 4.330 25.455 1180 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.26), residues: 1081 helix: 2.16 (0.27), residues: 370 sheet: 0.58 (0.33), residues: 259 loop : -1.55 (0.27), residues: 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.038 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 123 average time/residue: 0.1811 time to fit residues: 31.2583 Evaluate side-chains 115 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0925 time to fit residues: 1.8309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.0570 chunk 1 optimal weight: 120.0000 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.0170 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 53 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 8182 Z= 0.148 Angle : 0.489 6.050 11178 Z= 0.266 Chirality : 0.041 0.152 1327 Planarity : 0.003 0.040 1418 Dihedral : 3.891 26.015 1180 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.26), residues: 1081 helix: 2.40 (0.27), residues: 372 sheet: 0.59 (0.33), residues: 266 loop : -1.43 (0.28), residues: 443 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.000 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 120 average time/residue: 0.1783 time to fit residues: 30.4236 Evaluate side-chains 109 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4492 > 50: distance: 14 - 39: 20.794 distance: 18 - 44: 17.666 distance: 27 - 52: 23.359 distance: 30 - 39: 22.441 distance: 31 - 56: 11.981 distance: 39 - 40: 22.957 distance: 40 - 41: 48.729 distance: 40 - 43: 26.140 distance: 41 - 42: 46.160 distance: 41 - 44: 25.091 distance: 42 - 67: 20.869 distance: 44 - 45: 25.137 distance: 45 - 46: 26.402 distance: 45 - 48: 18.378 distance: 46 - 47: 16.427 distance: 46 - 52: 24.297 distance: 48 - 49: 24.029 distance: 49 - 50: 32.120 distance: 49 - 51: 14.136 distance: 52 - 53: 35.097 distance: 53 - 54: 10.507 distance: 54 - 55: 25.953 distance: 54 - 56: 14.239 distance: 56 - 57: 4.358 distance: 57 - 58: 29.492 distance: 57 - 60: 15.907 distance: 58 - 59: 8.396 distance: 58 - 67: 25.184 distance: 60 - 61: 28.096 distance: 61 - 62: 21.083 distance: 61 - 63: 18.362 distance: 62 - 64: 15.261 distance: 63 - 65: 22.935 distance: 65 - 66: 15.521 distance: 67 - 68: 7.052 distance: 68 - 69: 28.440 distance: 68 - 71: 30.691 distance: 69 - 70: 15.137 distance: 69 - 72: 27.681 distance: 72 - 73: 14.868 distance: 73 - 74: 21.725 distance: 73 - 76: 8.268 distance: 74 - 75: 21.310 distance: 74 - 79: 30.837 distance: 75 - 101: 18.558 distance: 76 - 77: 37.142 distance: 76 - 78: 23.982 distance: 79 - 80: 37.991 distance: 79 - 85: 25.425 distance: 80 - 81: 34.247 distance: 80 - 83: 4.504 distance: 81 - 82: 54.924 distance: 81 - 86: 29.067 distance: 82 - 109: 34.125 distance: 84 - 85: 56.279 distance: 86 - 87: 41.267 distance: 87 - 88: 42.854 distance: 87 - 90: 35.569 distance: 88 - 94: 40.584 distance: 89 - 117: 33.161 distance: 90 - 91: 5.393 distance: 91 - 92: 28.776 distance: 91 - 93: 48.490 distance: 94 - 95: 30.457 distance: 95 - 96: 33.029 distance: 95 - 98: 29.857 distance: 96 - 97: 44.624 distance: 96 - 101: 23.256 distance: 97 - 122: 30.256 distance: 98 - 99: 31.713 distance: 98 - 100: 28.984 distance: 101 - 102: 17.437 distance: 102 - 103: 27.716 distance: 102 - 105: 11.364 distance: 103 - 104: 23.271 distance: 103 - 109: 10.160 distance: 105 - 106: 23.656 distance: 105 - 107: 23.904 distance: 106 - 108: 36.155