Starting phenix.real_space_refine on Wed Jun 18 12:54:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sgz_25121/06_2025/7sgz_25121.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgz_25121/06_2025/7sgz_25121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sgz_25121/06_2025/7sgz_25121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgz_25121/06_2025/7sgz_25121.map" model { file = "/net/cci-nas-00/data/ceres_data/7sgz_25121/06_2025/7sgz_25121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgz_25121/06_2025/7sgz_25121.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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: 6 Type Number sf(0) Gaussians P 37 5.49 5 Mg 4 5.21 5 S 115 5.16 5 C 13246 2.51 5 N 3615 2.21 5 O 4038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 21055 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3416 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 401} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2489 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2569 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2617 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2693 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2178 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain breaks: 6 Chain: "G" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2313 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 4, 'TRANS': 287} Chain breaks: 1 Chain: "H" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2154 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 4 Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.96, per 1000 atoms: 0.66 Number of scatterers: 21055 At special positions: 0 Unit cell: (124.2, 125.028, 140.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 115 16.00 P 37 15.00 Mg 4 11.99 O 4038 8.00 N 3615 7.00 C 13246 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: 5.63 Conformation dependent library (CDL) restraints added in 3.0 seconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4898 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 16 sheets defined 52.2% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.736A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 161 through 175 removed outlier: 3.759A pdb=" N PHE A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.703A pdb=" N PHE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.536A pdb=" N MET A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 284 through 291 removed outlier: 4.032A pdb=" N LYS A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.621A pdb=" N MET A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.693A pdb=" N LEU A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 413 through 431 Processing helix chain 'A' and resid 432 through 435 removed outlier: 3.531A pdb=" N GLY A 435 " --> pdb=" O SER A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 445 through 468 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.842A pdb=" N ASN A 479 " --> pdb=" O HIS A 475 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.512A pdb=" N CYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 68 through 75 removed outlier: 4.079A pdb=" N VAL B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 98 removed outlier: 3.658A pdb=" N GLN B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 135 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.878A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.726A pdb=" N GLN B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 157' Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.960A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 89 through 101 removed outlier: 4.218A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.839A pdb=" N ALA C 121 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.683A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.509A pdb=" N LEU C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.151A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.553A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 217 " --> pdb=" O GLN C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 256 through 271 removed outlier: 4.046A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 313 Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.727A pdb=" N VAL D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 54 removed outlier: 3.568A pdb=" N VAL D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.467A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.393A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 193 through 209 removed outlier: 5.177A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 228 through 246 Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.554A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.520A pdb=" N ILE D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.620A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.150A pdb=" N THR E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 105 through 118 removed outlier: 3.514A pdb=" N ILE E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.675A pdb=" N LEU E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 148 through 161 Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 226 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 Processing helix chain 'E' and resid 295 through 308 removed outlier: 4.141A pdb=" N ILE E 299 " --> pdb=" O PRO E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 335 removed outlier: 3.635A pdb=" N LEU E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 354 Processing helix chain 'F' and resid 12 through 19 removed outlier: 4.193A pdb=" N TYR F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 30 removed outlier: 4.378A pdb=" N ILE F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 26 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 109 removed outlier: 3.761A pdb=" N LEU F 101 " --> pdb=" O CYS F 97 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL F 103 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 221 removed outlier: 3.679A pdb=" N ILE F 220 " --> pdb=" O GLN F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 257 removed outlier: 3.525A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 254 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 removed outlier: 4.389A pdb=" N CYS F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS F 420 " --> pdb=" O LYS F 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 26 removed outlier: 4.245A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 29 No H-bonds generated for 'chain 'G' and resid 27 through 29' Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 85 through 95 removed outlier: 3.884A pdb=" N ILE G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 93 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER G 94 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 160 through 174 removed outlier: 3.607A pdb=" N GLU G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY G 174 " --> pdb=" O LEU G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 249 removed outlier: 3.619A pdb=" N LYS G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 330 removed outlier: 3.982A pdb=" N GLU G 323 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU G 325 " --> pdb=" O GLN G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 27 removed outlier: 3.588A pdb=" N TRP H 16 " --> pdb=" O LYS H 12 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE H 26 " --> pdb=" O VAL H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 61 Processing helix chain 'H' and resid 98 through 103 removed outlier: 3.526A pdb=" N THR H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 209 Processing helix chain 'H' and resid 233 through 242 removed outlier: 3.623A pdb=" N LEU H 237 " --> pdb=" O ASN H 233 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN H 239 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 244 No H-bonds generated for 'chain 'H' and resid 243 through 244' Processing helix chain 'H' and resid 245 through 249 removed outlier: 3.660A pdb=" N VAL H 248 " --> pdb=" O ASN H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 339 removed outlier: 3.552A pdb=" N PHE H 332 " --> pdb=" O ASP H 328 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE H 333 " --> pdb=" O PHE H 329 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR H 334 " --> pdb=" O LYS H 330 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE H 335 " --> pdb=" O ASN H 331 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Proline residue: H 337 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.187A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 261 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 108 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 109 through 114 removed outlier: 5.923A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 82 removed outlier: 3.693A pdb=" N ILE C 114 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 49 " --> pdb=" O PHE C 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.708A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.332A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 93 through 96 removed outlier: 4.366A pdb=" N ASN E 141 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 73 through 76 removed outlier: 3.691A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 4 through 6 removed outlier: 7.081A pdb=" N LYS F 4 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR F 80 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG F 78 " --> pdb=" O ILE F 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 70 through 71 removed outlier: 3.863A pdb=" N CYS F 70 " --> pdb=" O ILE F 45 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE F 45 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 42 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA F 33 " --> pdb=" O CYS F 95 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS F 95 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.949A pdb=" N THR F 120 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY F 157 " --> pdb=" O LYS F 122 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR H 264 " --> pdb=" O LYS H 253 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE H 322 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 231 through 233 removed outlier: 3.688A pdb=" N HIS F 434 " --> pdb=" O CYS F 438 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS F 438 " --> pdb=" O HIS F 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 231 through 233 removed outlier: 3.688A pdb=" N HIS F 434 " --> pdb=" O CYS F 438 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS F 438 " --> pdb=" O HIS F 434 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL F 439 " --> pdb=" O ILE F 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 409 through 411 removed outlier: 3.910A pdb=" N ILE F 409 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 264 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS F 282 " --> pdb=" O MET F 265 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS F 291 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU F 293 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA G 13 " --> pdb=" O LEU G 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 80 through 84 removed outlier: 4.166A pdb=" N MET G 80 " --> pdb=" O ILE G 41 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE G 41 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU G 82 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL G 49 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 232 through 238 removed outlier: 4.051A pdb=" N GLU G 177 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE G 205 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE G 202 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR H 117 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 92 through 97 removed outlier: 6.908A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP H 42 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 43 " --> pdb=" O CYS H 52 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N CYS H 52 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 371 " --> pdb=" O MET H 364 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 2952 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: 7.74 Time building geometry restraints manager: 6.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6902 1.36 - 1.51: 5541 1.51 - 1.66: 8844 1.66 - 1.80: 85 1.80 - 1.95: 87 Bond restraints: 21459 Sorted by residual: bond pdb=" O3 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.79e+00 bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.52e+00 bond pdb=" O2 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.567 1.511 0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" O1 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 21454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 28396 1.44 - 2.88: 544 2.88 - 4.33: 106 4.33 - 5.77: 41 5.77 - 7.21: 12 Bond angle restraints: 29099 Sorted by residual: angle pdb=" CA LYS A 296 " pdb=" CB LYS A 296 " pdb=" CG LYS A 296 " ideal model delta sigma weight residual 114.10 121.15 -7.05 2.00e+00 2.50e-01 1.24e+01 angle pdb=" N GLU C 279 " pdb=" CA GLU C 279 " pdb=" CB GLU C 279 " ideal model delta sigma weight residual 110.22 115.57 -5.35 1.54e+00 4.22e-01 1.21e+01 angle pdb=" N THR G 29 " pdb=" CA THR G 29 " pdb=" C THR G 29 " ideal model delta sigma weight residual 109.81 116.82 -7.01 2.21e+00 2.05e-01 1.01e+01 angle pdb=" C THR H 300 " pdb=" N LYS H 320 " pdb=" CA LYS H 320 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.75e+00 angle pdb=" CA GLY A 349 " pdb=" C GLY A 349 " pdb=" N SER A 350 " ideal model delta sigma weight residual 114.23 116.71 -2.48 8.80e-01 1.29e+00 7.91e+00 ... (remaining 29094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 12708 35.06 - 70.12: 350 70.12 - 105.19: 20 105.19 - 140.25: 1 140.25 - 175.31: 1 Dihedral angle restraints: 13080 sinusoidal: 5570 harmonic: 7510 Sorted by residual: dihedral pdb=" O1B ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PB ADP E 402 " pdb=" PA ADP E 402 " ideal model delta sinusoidal sigma weight residual 300.00 179.88 120.12 1 2.00e+01 2.50e-03 3.60e+01 dihedral pdb=" C4' DA T 22 " pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " pdb=" P DG T 23 " ideal model delta sinusoidal sigma weight residual -140.00 35.31 -175.31 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASP A 87 " pdb=" C ASP A 87 " pdb=" N VAL A 88 " pdb=" CA VAL A 88 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 13077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3088 0.071 - 0.142: 269 0.142 - 0.212: 6 0.212 - 0.283: 0 0.283 - 0.354: 1 Chirality restraints: 3364 Sorted by residual: chirality pdb=" CB ILE G 251 " pdb=" CA ILE G 251 " pdb=" CG1 ILE G 251 " pdb=" CG2 ILE G 251 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB VAL F 110 " pdb=" CA VAL F 110 " pdb=" CG1 VAL F 110 " pdb=" CG2 VAL F 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR G 29 " pdb=" N THR G 29 " pdb=" C THR G 29 " pdb=" CB THR G 29 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 3361 not shown) Planarity restraints: 3585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 298 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO F 299 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO F 299 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 299 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 143 " -0.009 2.00e-02 2.50e+03 1.60e-02 4.49e+00 pdb=" CG PHE C 143 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE C 143 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE C 143 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C 143 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 143 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 42 " -0.012 2.00e-02 2.50e+03 1.23e-02 3.81e+00 pdb=" CG TRP H 42 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP H 42 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP H 42 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 42 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 42 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 42 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 42 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 42 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 42 " -0.001 2.00e-02 2.50e+03 ... (remaining 3582 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 358 2.68 - 3.24: 19758 3.24 - 3.79: 32659 3.79 - 4.35: 43072 4.35 - 4.90: 71532 Nonbonded interactions: 167379 Sorted by model distance: nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.128 2.170 nonbonded pdb=" OG1 THR D 72 " pdb="MG MG E 401 " model vdw 2.136 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.141 2.170 nonbonded pdb=" O3A AGS A 701 " pdb="MG MG A 702 " model vdw 2.144 2.170 nonbonded pdb=" O2B AGS D 500 " pdb=" O3G AGS D 500 " model vdw 2.202 3.040 ... (remaining 167374 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: 6.350 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: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 52.040 Find NCS groups from input model: 0.460 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 21459 Z= 0.113 Angle : 0.533 7.209 29099 Z= 0.273 Chirality : 0.040 0.354 3364 Planarity : 0.003 0.055 3585 Dihedral : 15.376 175.309 8182 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.04 % Allowed : 0.48 % Favored : 99.48 % Cbeta Deviations : 0.00 % 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: 0.10 (0.17), residues: 2516 helix: 0.92 (0.15), residues: 1167 sheet: 0.43 (0.27), residues: 453 loop : -1.22 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 42 HIS 0.009 0.001 HIS B 95 PHE 0.035 0.001 PHE C 143 TYR 0.013 0.001 TYR F 422 ARG 0.010 0.000 ARG B 157 Details of bonding type rmsd hydrogen bonds : bond 0.20148 ( 1017) hydrogen bonds : angle 7.25374 ( 2952) covalent geometry : bond 0.00230 (21459) covalent geometry : angle 0.53327 (29099) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 2.276 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.4026 (ppp) cc_final: 0.3670 (ptm) REVERT: F 241 GLU cc_start: 0.7240 (mp0) cc_final: 0.5624 (mp0) REVERT: F 242 PHE cc_start: 0.7400 (t80) cc_final: 0.7184 (t80) REVERT: G 36 ASP cc_start: 0.7259 (m-30) cc_final: 0.7039 (m-30) REVERT: G 64 ARG cc_start: 0.7544 (tmm-80) cc_final: 0.6512 (tpt90) REVERT: G 170 LEU cc_start: 0.7220 (tp) cc_final: 0.6916 (tp) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.3391 time to fit residues: 165.4868 Evaluate side-chains 247 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 8.9990 chunk 192 optimal weight: 0.0570 chunk 106 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 341 HIS ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 77 ASN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 148 ASN D 305 HIS D 352 GLN G 52 ASN G 88 HIS H 97 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.183425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.144248 restraints weight = 27876.660| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.62 r_work: 0.3695 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21459 Z= 0.184 Angle : 0.611 8.464 29099 Z= 0.316 Chirality : 0.044 0.204 3364 Planarity : 0.004 0.057 3585 Dihedral : 12.062 175.666 3076 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.21 % Allowed : 9.12 % Favored : 89.67 % Cbeta Deviations : 0.00 % 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: 0.20 (0.18), residues: 2516 helix: 1.07 (0.15), residues: 1167 sheet: 0.39 (0.26), residues: 474 loop : -1.25 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 42 HIS 0.008 0.001 HIS A 257 PHE 0.023 0.002 PHE A 456 TYR 0.023 0.002 TYR F 256 ARG 0.006 0.001 ARG F 20 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 1017) hydrogen bonds : angle 5.23326 ( 2952) covalent geometry : bond 0.00430 (21459) covalent geometry : angle 0.61078 (29099) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.6534 (ttmt) cc_final: 0.6229 (tppt) REVERT: C 284 ILE cc_start: 0.8790 (tt) cc_final: 0.8418 (mp) REVERT: D 115 ARG cc_start: 0.7542 (mtp85) cc_final: 0.7316 (mtm-85) REVERT: D 123 LYS cc_start: 0.8055 (pttp) cc_final: 0.7792 (tppt) REVERT: E 71 ASP cc_start: 0.7462 (p0) cc_final: 0.7182 (p0) REVERT: E 207 THR cc_start: 0.8234 (m) cc_final: 0.7917 (p) REVERT: E 273 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6957 (mt-10) REVERT: G 36 ASP cc_start: 0.7622 (m-30) cc_final: 0.7322 (m-30) REVERT: G 96 MET cc_start: 0.6570 (pmm) cc_final: 0.6192 (pmm) outliers start: 28 outliers final: 19 residues processed: 289 average time/residue: 0.3870 time to fit residues: 170.2901 Evaluate side-chains 254 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 61 optimal weight: 0.6980 chunk 181 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 0.0980 chunk 150 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 ASN D 305 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.184038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.145285 restraints weight = 27647.106| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.59 r_work: 0.3683 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21459 Z= 0.119 Angle : 0.519 7.205 29099 Z= 0.268 Chirality : 0.040 0.193 3364 Planarity : 0.003 0.053 3585 Dihedral : 11.902 174.694 3076 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.30 % Allowed : 12.15 % Favored : 86.55 % Cbeta Deviations : 0.00 % 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: 0.39 (0.18), residues: 2516 helix: 1.30 (0.16), residues: 1177 sheet: 0.32 (0.25), residues: 482 loop : -1.23 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 42 HIS 0.013 0.001 HIS D 305 PHE 0.021 0.001 PHE A 279 TYR 0.014 0.001 TYR F 256 ARG 0.003 0.000 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 1017) hydrogen bonds : angle 4.89341 ( 2952) covalent geometry : bond 0.00265 (21459) covalent geometry : angle 0.51893 (29099) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 2.352 Fit side-chains revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7619 (mmtm) cc_final: 0.7322 (mmtt) REVERT: C 45 LYS cc_start: 0.6541 (ttmt) cc_final: 0.6216 (tppt) REVERT: C 284 ILE cc_start: 0.8738 (tt) cc_final: 0.8341 (mm) REVERT: D 115 ARG cc_start: 0.7362 (mtp85) cc_final: 0.7159 (mtm-85) REVERT: D 123 LYS cc_start: 0.8056 (pttp) cc_final: 0.7809 (tppt) REVERT: D 209 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7390 (p0) REVERT: D 227 ASP cc_start: 0.8461 (p0) cc_final: 0.8241 (p0) REVERT: E 207 THR cc_start: 0.8128 (m) cc_final: 0.7798 (p) REVERT: E 216 LYS cc_start: 0.7819 (mttm) cc_final: 0.7478 (mptt) REVERT: E 273 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6924 (mt-10) REVERT: F 241 GLU cc_start: 0.6961 (mp0) cc_final: 0.5925 (mp0) REVERT: G 36 ASP cc_start: 0.7733 (m-30) cc_final: 0.7466 (m-30) REVERT: G 121 PHE cc_start: 0.7038 (m-80) cc_final: 0.6709 (m-80) REVERT: G 312 GLU cc_start: 0.7296 (tt0) cc_final: 0.7065 (tt0) outliers start: 30 outliers final: 18 residues processed: 275 average time/residue: 0.3534 time to fit residues: 148.7026 Evaluate side-chains 254 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 149 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 53.986 > 50: distance: 55 - 93: 9.240 distance: 58 - 90: 6.692 distance: 81 - 82: 5.295 distance: 82 - 83: 13.525 distance: 82 - 85: 10.562 distance: 83 - 84: 3.977 distance: 83 - 90: 17.472 distance: 85 - 86: 8.651 distance: 86 - 87: 9.531 distance: 87 - 88: 9.194 distance: 88 - 89: 12.888 distance: 90 - 91: 10.671 distance: 91 - 92: 15.687 distance: 91 - 94: 6.276 distance: 92 - 93: 8.081 distance: 92 - 97: 8.621 distance: 94 - 95: 17.962 distance: 94 - 96: 12.547 distance: 97 - 103: 10.806 distance: 98 - 99: 5.641 distance: 98 - 101: 3.345 distance: 99 - 100: 17.079 distance: 99 - 104: 9.181 distance: 101 - 102: 6.130 distance: 102 - 103: 10.307 distance: 104 - 105: 4.917 distance: 105 - 106: 5.780 distance: 105 - 108: 11.078 distance: 106 - 107: 17.007 distance: 106 - 111: 10.036 distance: 108 - 109: 25.662 distance: 108 - 110: 41.641 distance: 111 - 112: 6.504 distance: 113 - 114: 13.568 distance: 113 - 120: 17.372 distance: 115 - 116: 7.938 distance: 116 - 117: 7.088 distance: 117 - 118: 9.888 distance: 118 - 119: 16.006 distance: 120 - 121: 7.076 distance: 121 - 122: 6.669 distance: 121 - 124: 7.229 distance: 122 - 123: 18.608 distance: 122 - 128: 19.425 distance: 124 - 125: 20.807 distance: 125 - 126: 15.631 distance: 125 - 127: 17.424 distance: 128 - 129: 16.504 distance: 129 - 130: 15.972 distance: 129 - 132: 27.281 distance: 130 - 131: 11.059 distance: 130 - 136: 17.465 distance: 132 - 133: 17.318 distance: 133 - 134: 22.449 distance: 133 - 135: 42.177 distance: 137 - 138: 11.765 distance: 137 - 140: 3.100 distance: 138 - 139: 6.763 distance: 138 - 147: 7.640 distance: 140 - 141: 6.969 distance: 141 - 143: 7.729 distance: 142 - 144: 6.419 distance: 143 - 145: 7.731 distance: 144 - 146: 4.407 distance: 145 - 146: 3.727 distance: 147 - 148: 4.192 distance: 148 - 149: 7.552 distance: 148 - 151: 5.307 distance: 149 - 150: 6.891 distance: 149 - 158: 11.865 distance: 151 - 152: 8.551 distance: 152 - 153: 7.151 distance: 153 - 154: 9.642 distance: 154 - 155: 9.991 distance: 155 - 156: 9.572 distance: 158 - 159: 5.294 distance: 159 - 162: 3.994 distance: 160 - 161: 8.608