Starting phenix.real_space_refine on Tue Jul 23 07:05:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/07_2024/8fs4_29413_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/07_2024/8fs4_29413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/07_2024/8fs4_29413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/07_2024/8fs4_29413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/07_2024/8fs4_29413_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/07_2024/8fs4_29413_neut.cif" } resolution = 2.94 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= 0.028 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 55 5.49 5 Mg 4 5.21 5 S 112 5.16 5 C 13352 2.51 5 N 3657 2.21 5 O 4111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 64": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "G GLU 131": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 21291 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3466 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 16, 'TRANS': 406} Chain breaks: 3 Chain: "B" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2482 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 1 Chain: "C" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2593 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2760 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 334} Chain breaks: 1 Chain: "F" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2184 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 8, 'TRANS': 261} Chain breaks: 10 Chain: "G" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2265 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 4, 'TRANS': 281} Chain breaks: 3 Chain: "H" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1930 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 7, 'TRANS': 229} Chain breaks: 9 Chain: "I" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 488 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 2 Chain: "J" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 151 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} 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: 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: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.70, per 1000 atoms: 0.60 Number of scatterers: 21291 At special positions: 0 Unit cell: (117.576, 136.62, 138.276, 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 112 16.00 P 55 15.00 Mg 4 11.99 O 4111 8.00 N 3657 7.00 C 13352 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.72 Conformation dependent library (CDL) restraints added in 4.0 seconds 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4860 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 16 sheets defined 52.9% alpha, 14.4% beta 15 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 7.37 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.621A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 194 through 210 Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 297 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 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.914A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) 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 409 removed outlier: 3.613A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 432 removed outlier: 4.170A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 471 removed outlier: 3.614A pdb=" N ASP A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 483 through 498 Proline residue: A 489 - end of helix removed outlier: 3.800A pdb=" N SER A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.520A pdb=" N ILE B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.566A pdb=" N VAL B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 61 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 93 through 99 removed outlier: 3.517A pdb=" N ALA B 97 " --> pdb=" O ILE B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.854A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.807A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.522A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.728A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.531A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.570A pdb=" N SER B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.665A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.577A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.861A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.718A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.033A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.529A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (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 255 through 271 removed outlier: 4.065A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 4.014A pdb=" N LEU C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.938A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 334 removed outlier: 3.720A pdb=" N GLY C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 30 Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.710A pdb=" N VAL D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.526A pdb=" N VAL D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.995A 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: 4.284A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.975A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) 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 152 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.557A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.546A pdb=" N ARG D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.777A pdb=" N LEU D 235 " --> pdb=" O GLY D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 296 through 311 Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.559A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.810A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.366A 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 62 Processing helix chain 'E' and resid 98 through 103 removed outlier: 7.297A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.967A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.708A 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 153 through 161 removed outlier: 3.832A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 217 through 227 removed outlier: 3.531A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 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 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.544A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.639A pdb=" N THR F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 113 removed outlier: 4.202A pdb=" N LEU F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 Processing helix chain 'F' and resid 240 through 252 removed outlier: 4.206A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 412 through 424 Processing helix chain 'G' and resid 17 through 27 removed outlier: 4.096A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) 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 86 through 97 removed outlier: 3.758A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 245 through 250 Processing helix chain 'G' and resid 321 through 329 Processing helix chain 'H' and resid 9 through 27 Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 98 through 105 removed outlier: 3.894A pdb=" N THR H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE H 104 " --> pdb=" O HIS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 243 removed outlier: 3.876A pdb=" N LEU H 237 " --> pdb=" O ASN H 233 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN H 243 " --> pdb=" O ASN H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 336 removed outlier: 4.130A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.134A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 105 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE A 223 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 107 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 108 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA3, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.133A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 186 removed outlier: 7.587A pdb=" N LYS B 185 " --> pdb=" O VAL B 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.099A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.244A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.216A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 76 removed outlier: 6.825A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'F' and resid 91 through 92 removed outlier: 3.730A pdb=" N ILE F 465 " --> pdb=" O TRP F 69 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 153 through 160 Processing sheet with id=AB3, first strand: chain 'F' and resid 406 through 411 removed outlier: 4.401A pdb=" N LEU F 281 " --> pdb=" O TRP F 296 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS F 291 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU G 122 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER G 69 " --> pdb=" O SER G 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 79 through 85 removed outlier: 7.081A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP G 42 " --> pdb=" O GLY G 45 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY G 45 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP G 260 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 232 through 238 removed outlier: 3.590A pdb=" N ALA G 193 " --> pdb=" O TYR G 181 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU G 189 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR H 148 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL H 136 " --> pdb=" O TYR H 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 153 through 155 removed outlier: 3.995A pdb=" N SER H 93 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 284 through 289 removed outlier: 3.507A pdb=" N SER H 262 " --> pdb=" O GLU H 255 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 3039 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 7.41 Time building geometry restraints manager: 9.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6893 1.36 - 1.50: 5704 1.50 - 1.65: 8957 1.65 - 1.80: 78 1.80 - 1.95: 90 Bond restraints: 21722 Sorted by residual: bond pdb=" N GLN D 25 " pdb=" CA GLN D 25 " ideal model delta sigma weight residual 1.455 1.487 -0.033 9.60e-03 1.09e+04 1.16e+01 bond pdb=" CG1 ILE H 335 " pdb=" CD1 ILE H 335 " ideal model delta sigma weight residual 1.513 1.390 0.123 3.90e-02 6.57e+02 9.96e+00 bond pdb=" N ILE F 121 " pdb=" CA ILE F 121 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.40e+00 bond pdb=" N VAL F 7 " pdb=" CA VAL F 7 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.19e-02 7.06e+03 9.24e+00 bond pdb=" N ILE F 72 " pdb=" CA ILE F 72 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.01e-02 9.80e+03 8.86e+00 ... (remaining 21717 not shown) Histogram of bond angle deviations from ideal: 97.52 - 105.33: 467 105.33 - 113.13: 12320 113.13 - 120.94: 10570 120.94 - 128.74: 5991 128.74 - 136.55: 153 Bond angle restraints: 29501 Sorted by residual: angle pdb=" N LYS D 30 " pdb=" CA LYS D 30 " pdb=" C LYS D 30 " ideal model delta sigma weight residual 114.31 108.23 6.08 1.29e+00 6.01e-01 2.22e+01 angle pdb=" CA LYS C 112 " pdb=" C LYS C 112 " pdb=" O LYS C 112 " ideal model delta sigma weight residual 121.72 116.94 4.78 1.18e+00 7.18e-01 1.64e+01 angle pdb=" N LEU E 242 " pdb=" CA LEU E 242 " pdb=" C LEU E 242 " ideal model delta sigma weight residual 112.72 107.84 4.88 1.28e+00 6.10e-01 1.46e+01 angle pdb=" N LYS A 291 " pdb=" CA LYS A 291 " pdb=" C LYS A 291 " ideal model delta sigma weight residual 112.89 108.27 4.62 1.24e+00 6.50e-01 1.39e+01 angle pdb=" CA PHE G 31 " pdb=" C PHE G 31 " pdb=" O PHE G 31 " ideal model delta sigma weight residual 122.64 117.99 4.65 1.25e+00 6.40e-01 1.38e+01 ... (remaining 29496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 12490 35.46 - 70.91: 633 70.91 - 106.37: 27 106.37 - 141.82: 1 141.82 - 177.28: 2 Dihedral angle restraints: 13153 sinusoidal: 5713 harmonic: 7440 Sorted by residual: dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 117.28 -177.28 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 85.27 -145.27 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 61.01 -121.01 1 2.00e+01 2.50e-03 3.64e+01 ... (remaining 13150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3241 0.103 - 0.206: 177 0.206 - 0.308: 1 0.308 - 0.411: 0 0.411 - 0.514: 1 Chirality restraints: 3420 Sorted by residual: chirality pdb=" P DT I 34 " pdb=" OP1 DT I 34 " pdb=" OP2 DT I 34 " pdb=" O5' DT I 34 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CA ILE F 121 " pdb=" N ILE F 121 " pdb=" C ILE F 121 " pdb=" CB ILE F 121 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE G 304 " pdb=" N ILE G 304 " pdb=" C ILE G 304 " pdb=" CB ILE G 304 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 3417 not shown) Planarity restraints: 3557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 336 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.62e+00 pdb=" N PRO H 337 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO H 337 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 337 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 470 " 0.186 9.50e-02 1.11e+02 8.36e-02 4.28e+00 pdb=" NE ARG F 470 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG F 470 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 470 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 470 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 224 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C GLU C 224 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU C 224 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP C 225 " 0.012 2.00e-02 2.50e+03 ... (remaining 3554 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 73 2.45 - 3.06: 13992 3.06 - 3.67: 32655 3.67 - 4.29: 49372 4.29 - 4.90: 82708 Nonbonded interactions: 178800 Sorted by model distance: nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 1.835 2.170 nonbonded pdb=" O2B AGS D 401 " pdb="MG MG D 402 " model vdw 1.899 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 1.907 2.170 nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.093 2.170 nonbonded pdb=" OE1 GLU B 301 " pdb=" OH TYR C 308 " model vdw 2.201 2.440 ... (remaining 178795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 4.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.150 Set scattering table: 0.230 Process input model: 64.690 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 : 0.004 0.123 21722 Z= 0.288 Angle : 0.654 8.148 29501 Z= 0.387 Chirality : 0.045 0.514 3420 Planarity : 0.004 0.084 3557 Dihedral : 18.513 177.279 8293 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.69 % Allowed : 27.31 % Favored : 70.00 % 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: -0.22 (0.18), residues: 2469 helix: 0.53 (0.16), residues: 1214 sheet: -0.21 (0.25), residues: 504 loop : -1.02 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 66 HIS 0.011 0.001 HIS E 18 PHE 0.012 0.001 PHE H 66 TYR 0.018 0.001 TYR G 181 ARG 0.006 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 245 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.4205 (tpt) cc_final: 0.3260 (mtt) REVERT: B 145 ASN cc_start: 0.8774 (m-40) cc_final: 0.8471 (m-40) REVERT: C 104 ARG cc_start: 0.6938 (ttp80) cc_final: 0.6738 (mtp85) REVERT: F 472 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7625 (tttp) REVERT: G 64 ARG cc_start: 0.7164 (ttm170) cc_final: 0.6703 (mtp180) REVERT: G 151 ARG cc_start: 0.6231 (tpp-160) cc_final: 0.4979 (tpt170) outliers start: 62 outliers final: 54 residues processed: 303 average time/residue: 1.1386 time to fit residues: 398.8771 Evaluate side-chains 281 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 227 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain H residue 256 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 0.0470 chunk 229 optimal weight: 0.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 366 ASN A 411 ASN A 436 HIS C 333 ASN D 255 GLN D 311 ASN D 340 HIS E 144 ASN E 243 ASN E 244 ASN F 8 ASN G 190 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 21722 Z= 0.230 Angle : 0.570 7.970 29501 Z= 0.300 Chirality : 0.043 0.196 3420 Planarity : 0.004 0.057 3557 Dihedral : 14.899 165.586 3307 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.30 % Allowed : 24.75 % Favored : 70.95 % 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: 0.24 (0.18), residues: 2469 helix: 0.89 (0.16), residues: 1204 sheet: -0.08 (0.24), residues: 507 loop : -0.66 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 42 HIS 0.007 0.001 HIS B 232 PHE 0.017 0.002 PHE H 66 TYR 0.014 0.001 TYR F 80 ARG 0.011 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 278 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.6908 (t) cc_final: 0.6601 (p) REVERT: A 273 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7159 (mp) REVERT: B 50 MET cc_start: 0.7149 (ppp) cc_final: 0.6880 (ppp) REVERT: B 157 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7646 (mtt-85) REVERT: C 39 LYS cc_start: 0.7683 (mtpp) cc_final: 0.7457 (ttmt) REVERT: C 293 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7258 (tm-30) REVERT: D 123 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7266 (mttt) REVERT: D 159 THR cc_start: 0.8842 (m) cc_final: 0.8631 (m) REVERT: E 96 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6971 (pt) REVERT: E 212 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6098 (tt0) REVERT: E 220 LYS cc_start: 0.8080 (tppp) cc_final: 0.7498 (mppt) REVERT: E 314 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8223 (p0) REVERT: F 19 LEU cc_start: 0.7730 (tt) cc_final: 0.7425 (tp) REVERT: F 472 LYS cc_start: 0.7944 (ttmm) cc_final: 0.7586 (tttp) REVERT: G 151 ARG cc_start: 0.6330 (tpp-160) cc_final: 0.5118 (tpt170) REVERT: G 176 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7095 (pttt) REVERT: H 335 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6530 (mp) outliers start: 99 outliers final: 43 residues processed: 339 average time/residue: 1.1575 time to fit residues: 452.8968 Evaluate side-chains 292 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 241 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.6593 > 50: distance: 67 - 72: 35.284 distance: 74 - 76: 32.384 distance: 75 - 98: 48.424 distance: 76 - 77: 9.235 distance: 77 - 80: 25.281 distance: 78 - 79: 43.482 distance: 78 - 85: 19.445 distance: 80 - 81: 33.403 distance: 81 - 82: 18.171 distance: 82 - 83: 22.168 distance: 83 - 84: 17.798 distance: 86 - 89: 20.125 distance: 87 - 88: 25.120 distance: 87 - 92: 6.557 distance: 88 - 113: 14.004 distance: 89 - 90: 19.987 distance: 89 - 91: 34.969 distance: 92 - 93: 13.227 distance: 93 - 94: 20.612 distance: 93 - 96: 4.091 distance: 94 - 95: 7.764 distance: 94 - 98: 19.608 distance: 95 - 120: 7.856 distance: 96 - 97: 31.339 distance: 98 - 99: 12.467 distance: 99 - 100: 36.687 distance: 99 - 102: 17.372 distance: 100 - 101: 18.533 distance: 100 - 105: 19.942 distance: 101 - 125: 44.445 distance: 102 - 104: 8.538 distance: 105 - 106: 16.902 distance: 106 - 107: 4.634 distance: 106 - 109: 16.345 distance: 107 - 108: 39.661 distance: 107 - 113: 38.494 distance: 108 - 133: 17.465 distance: 109 - 110: 18.000 distance: 109 - 111: 30.342 distance: 110 - 112: 54.340 distance: 113 - 114: 23.450 distance: 114 - 115: 25.216 distance: 114 - 117: 16.753 distance: 115 - 116: 7.155 distance: 115 - 120: 12.481 distance: 116 - 138: 8.261 distance: 117 - 118: 12.420 distance: 120 - 121: 5.081 distance: 121 - 122: 19.188 distance: 121 - 124: 18.502 distance: 122 - 123: 14.577 distance: 122 - 125: 18.601 distance: 123 - 149: 27.074 distance: 125 - 126: 4.179 distance: 126 - 127: 16.525 distance: 126 - 129: 28.250 distance: 127 - 128: 18.335 distance: 127 - 133: 8.530 distance: 128 - 156: 35.159 distance: 129 - 130: 27.281 distance: 130 - 131: 33.576 distance: 130 - 132: 40.759 distance: 133 - 134: 5.063 distance: 134 - 135: 15.359 distance: 134 - 137: 5.754 distance: 135 - 136: 28.447 distance: 135 - 138: 19.227 distance: 136 - 163: 26.126