Starting phenix.real_space_refine on Fri Aug 22 23:05:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xau_33099/08_2025/7xau_33099.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xau_33099/08_2025/7xau_33099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xau_33099/08_2025/7xau_33099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xau_33099/08_2025/7xau_33099.map" model { file = "/net/cci-nas-00/data/ceres_data/7xau_33099/08_2025/7xau_33099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xau_33099/08_2025/7xau_33099.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.101 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 54 5.16 5 C 5351 2.51 5 N 1437 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8443 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1923 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 12, 'TYR:plan': 1, 'ARG:plan': 7, 'ASP:plan': 3, 'GLU:plan': 2, 'TRP:plan': 3, 'ASN:plan1': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 178 Chain: "B" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1598 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 6, 'HIS:plan': 1, 'ARG:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 119 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Classifications: {'peptide': 3} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 2} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Time building chain proxies: 1.61, per 1000 atoms: 0.19 Number of scatterers: 8443 At special positions: 0 Unit cell: (87.74, 123.05, 123.05, 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 54 16.00 O 1601 8.00 N 1437 7.00 C 5351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.05 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.03 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 Links applied TRANS " DTR F 4 " - " PHE F 3 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 416.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN F 1 " pdb=" CB DTR F 4 " Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 32.1% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.648A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.880A pdb=" N ILE A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.820A pdb=" N ILE A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 removed outlier: 3.874A pdb=" N LEU A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.824A pdb=" N MET A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.548A pdb=" N THR A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TRP A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 168 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.969A pdb=" N TYR A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 removed outlier: 4.036A pdb=" N ILE A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.582A pdb=" N ILE A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 removed outlier: 4.131A pdb=" N ILE A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.620A pdb=" N VAL A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.625A pdb=" N SER A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 261 " --> pdb=" O MET A 257 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.606A pdb=" N ASN A 276 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 277 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 removed outlier: 3.841A pdb=" N ASP A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 314 Proline residue: A 309 - end of helix removed outlier: 3.514A pdb=" N TYR A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 326 removed outlier: 3.710A pdb=" N LYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 24 removed outlier: 3.615A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.637A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.651A pdb=" N SER B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.910A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 removed outlier: 3.906A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 removed outlier: 5.173A pdb=" N CYS B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 351 removed outlier: 4.133A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.525A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA C 21 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 7 through 24 removed outlier: 3.768A pdb=" N GLN D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.558A pdb=" N TYR D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 191 through 193 No H-bonds generated for 'chain 'E' and resid 191 through 193' Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 184 removed outlier: 4.129A pdb=" N ARG A 184 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 188 removed outlier: 6.138A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 52 removed outlier: 5.622A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 338 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 4.048A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.025A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.650A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 191 through 192 Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.493A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.645A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.514A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 51 removed outlier: 6.507A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.704A pdb=" N CYS E 159 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE E 212 " --> pdb=" O CYS E 159 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.431A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 243 " --> pdb=" O TYR E 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'E' and resid 189 through 190 286 hydrogen bonds defined for protein. 792 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: 0.83 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2336 1.33 - 1.46: 2330 1.46 - 1.59: 3865 1.59 - 1.71: 0 1.71 - 1.84: 74 Bond restraints: 8605 Sorted by residual: bond pdb=" CA GLU C 138 " pdb=" CB GLU C 138 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.34e-02 5.57e+03 2.48e+01 bond pdb=" C LEU A 270 " pdb=" N PRO A 271 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" CG LEU C 95 " pdb=" CD1 LEU C 95 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.94e+00 bond pdb=" C THR C 243 " pdb=" N GLY C 244 " ideal model delta sigma weight residual 1.332 1.319 0.013 5.00e-03 4.00e+04 6.57e+00 bond pdb=" C CYS C 148 " pdb=" N CYS C 149 " ideal model delta sigma weight residual 1.330 1.365 -0.035 1.39e-02 5.18e+03 6.41e+00 ... (remaining 8600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 11296 2.66 - 5.32: 361 5.32 - 7.98: 50 7.98 - 10.64: 6 10.64 - 13.29: 4 Bond angle restraints: 11717 Sorted by residual: angle pdb=" N LYS A 73 " pdb=" CA LYS A 73 " pdb=" C LYS A 73 " ideal model delta sigma weight residual 111.71 104.67 7.04 1.34e+00 5.57e-01 2.76e+01 angle pdb=" N MET B 243 " pdb=" CA MET B 243 " pdb=" C MET B 243 " ideal model delta sigma weight residual 113.41 107.18 6.23 1.22e+00 6.72e-01 2.60e+01 angle pdb=" N ALA A 72 " pdb=" CA ALA A 72 " pdb=" C ALA A 72 " ideal model delta sigma weight residual 110.53 116.64 -6.11 1.29e+00 6.01e-01 2.24e+01 angle pdb=" N VAL B 201 " pdb=" CA VAL B 201 " pdb=" C VAL B 201 " ideal model delta sigma weight residual 106.21 111.16 -4.95 1.07e+00 8.73e-01 2.14e+01 angle pdb=" C GLN A 187 " pdb=" N TRP A 188 " pdb=" CA TRP A 188 " ideal model delta sigma weight residual 122.46 128.81 -6.35 1.41e+00 5.03e-01 2.03e+01 ... (remaining 11712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4563 17.69 - 35.38: 428 35.38 - 53.07: 68 53.07 - 70.76: 10 70.76 - 88.45: 4 Dihedral angle restraints: 5073 sinusoidal: 1769 harmonic: 3304 Sorted by residual: dihedral pdb=" CA LEU A 105 " pdb=" C LEU A 105 " pdb=" N VAL A 106 " pdb=" CA VAL A 106 " ideal model delta harmonic sigma weight residual 180.00 -134.41 -45.59 0 5.00e+00 4.00e-02 8.31e+01 dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.62 -66.62 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CA TYR A 71 " pdb=" C TYR A 71 " pdb=" N ALA A 72 " pdb=" CA ALA A 72 " ideal model delta harmonic sigma weight residual -180.00 -145.55 -34.45 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 5070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 957 0.057 - 0.113: 322 0.113 - 0.169: 80 0.169 - 0.226: 19 0.226 - 0.282: 8 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CB VAL B 218 " pdb=" CA VAL B 218 " pdb=" CG1 VAL B 218 " pdb=" CG2 VAL B 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE C 270 " pdb=" CA ILE C 270 " pdb=" CG1 ILE C 270 " pdb=" CG2 ILE C 270 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL B 339 " pdb=" CA VAL B 339 " pdb=" CG1 VAL B 339 " pdb=" CG2 VAL B 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1383 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 175 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO A 176 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO C 236 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 308 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO A 309 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.037 5.00e-02 4.00e+02 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 981 2.73 - 3.27: 7741 3.27 - 3.81: 14228 3.81 - 4.36: 17133 4.36 - 4.90: 29082 Nonbonded interactions: 69165 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.187 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.215 3.040 nonbonded pdb=" O THR B 260 " pdb=" OG1 THR B 316 " model vdw 2.252 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.277 3.040 ... (remaining 69160 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.140 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 : 0.011 0.087 8610 Z= 0.478 Angle : 1.189 13.295 11728 Z= 0.695 Chirality : 0.063 0.282 1386 Planarity : 0.007 0.073 1490 Dihedral : 14.129 88.451 2924 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.17 % Allowed : 10.04 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.69 (0.19), residues: 1121 helix: -4.59 (0.13), residues: 322 sheet: -1.96 (0.28), residues: 272 loop : -2.65 (0.22), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 154 TYR 0.033 0.003 TYR C 59 PHE 0.037 0.004 PHE C 234 TRP 0.023 0.004 TRP C 99 HIS 0.008 0.002 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.01061 ( 8605) covalent geometry : angle 1.18831 (11717) SS BOND : bond 0.01320 ( 4) SS BOND : angle 2.35036 ( 8) hydrogen bonds : bond 0.30934 ( 286) hydrogen bonds : angle 11.55558 ( 792) link_TRANS : bond 0.00397 ( 1) link_TRANS : angle 0.35169 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7460 (m-80) cc_final: 0.7131 (m-80) REVERT: A 75 LYS cc_start: 0.6087 (mmtm) cc_final: 0.5728 (tptt) REVERT: C 327 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7750 (m) REVERT: E 6 GLU cc_start: 0.7745 (pm20) cc_final: 0.7446 (pm20) outliers start: 10 outliers final: 4 residues processed: 204 average time/residue: 0.4696 time to fit residues: 102.9651 Evaluate side-chains 148 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.5509 > 50: distance: 118 - 162: 11.299 distance: 121 - 159: 8.922 distance: 140 - 146: 21.724 distance: 146 - 147: 3.430 distance: 147 - 148: 4.590 distance: 147 - 150: 20.356 distance: 148 - 149: 11.526 distance: 148 - 152: 5.663 distance: 150 - 151: 5.339 distance: 152 - 153: 13.988 distance: 152 - 158: 22.955 distance: 153 - 154: 11.314 distance: 153 - 156: 7.358 distance: 154 - 155: 15.900 distance: 154 - 159: 6.447 distance: 156 - 157: 18.756 distance: 157 - 158: 32.619 distance: 159 - 160: 7.173 distance: 160 - 161: 13.147 distance: 160 - 163: 9.618 distance: 161 - 162: 4.194 distance: 161 - 168: 8.239 distance: 163 - 164: 23.462 distance: 164 - 165: 15.382 distance: 165 - 166: 9.503 distance: 165 - 167: 11.353 distance: 168 - 169: 5.283 distance: 169 - 170: 7.189 distance: 169 - 172: 6.821 distance: 170 - 171: 14.234 distance: 170 - 176: 37.766 distance: 172 - 173: 17.759 distance: 173 - 174: 6.777 distance: 173 - 175: 8.627 distance: 176 - 177: 26.521 distance: 177 - 178: 5.685 distance: 177 - 180: 13.039 distance: 178 - 179: 22.724 distance: 178 - 184: 12.935 distance: 180 - 181: 19.694 distance: 181 - 182: 22.677 distance: 181 - 183: 3.539 distance: 184 - 185: 11.144 distance: 185 - 186: 5.472 distance: 185 - 188: 19.163 distance: 186 - 187: 17.831 distance: 186 - 192: 14.188 distance: 188 - 189: 22.122 distance: 188 - 190: 23.519 distance: 189 - 191: 22.801 distance: 192 - 232: 5.851 distance: 193 - 194: 3.247 distance: 193 - 196: 11.162 distance: 194 - 195: 7.205 distance: 194 - 204: 6.848 distance: 195 - 229: 7.743 distance: 196 - 197: 6.382 distance: 197 - 198: 11.489 distance: 197 - 199: 7.760 distance: 198 - 200: 20.179 distance: 199 - 201: 15.886 distance: 200 - 202: 7.233 distance: 201 - 202: 8.705 distance: 202 - 203: 5.564 distance: 204 - 205: 10.532 distance: 205 - 206: 13.912 distance: 205 - 208: 15.929 distance: 206 - 207: 9.580 distance: 206 - 215: 16.213 distance: 208 - 209: 14.622 distance: 209 - 210: 14.683 distance: 210 - 211: 21.270 distance: 211 - 212: 5.654 distance: 212 - 213: 7.651 distance: 212 - 214: 6.364 distance: 215 - 216: 20.346 distance: 216 - 217: 30.499 distance: 216 - 219: 22.433 distance: 217 - 218: 25.542 distance: 217 - 223: 23.598 distance: 219 - 220: 19.282 distance: 220 - 221: 33.016 distance: 221 - 222: 29.372 distance: 223 - 224: 28.811 distance: 224 - 225: 28.693 distance: 224 - 227: 22.278 distance: 225 - 226: 15.712 distance: 225 - 229: 22.863 distance: 227 - 228: 18.184