Starting phenix.real_space_refine on Tue Jul 23 19:52:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/07_2024/8dvi_27739_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/07_2024/8dvi_27739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/07_2024/8dvi_27739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/07_2024/8dvi_27739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/07_2024/8dvi_27739_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/07_2024/8dvi_27739_neut.cif" } resolution = 3.2 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= 0.004 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 32 5.49 5 Mg 5 5.21 5 S 132 5.16 5 C 14995 2.51 5 N 3943 2.21 5 O 4586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 158": "OE1" <-> "OE2" Residue "H GLU 174": "OE1" <-> "OE2" Residue "H GLU 177": "OE1" <-> "OE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H GLU 211": "OE1" <-> "OE2" Residue "H GLU 223": "OE1" <-> "OE2" Residue "H GLU 234": "OE1" <-> "OE2" Residue "H GLU 243": "OE1" <-> "OE2" Residue "H GLU 256": "OE1" <-> "OE2" Residue "H GLU 271": "OE1" <-> "OE2" Residue "H GLU 289": "OE1" <-> "OE2" Residue "H GLU 311": "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: 23693 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "H" Number of atoms: 2644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2644 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain breaks: 1 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} 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: 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: "F" 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} Time building chain proxies: 12.70, per 1000 atoms: 0.54 Number of scatterers: 23693 At special positions: 0 Unit cell: (134.136, 130.824, 142.416, 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 132 16.00 P 32 15.00 Mg 5 11.99 O 4586 8.00 N 3943 7.00 C 14995 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: 9.62 Conformation dependent library (CDL) restraints added in 4.6 seconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 20 sheets defined 53.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 86 through 118 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.527A pdb=" N GLY A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.520A pdb=" N ILE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.550A pdb=" N LYS A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.542A pdb=" N TYR B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 28' Processing helix chain 'B' and resid 31 through 48 Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 88 through 119 removed outlier: 3.529A pdb=" N LEU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 176 through 184 removed outlier: 3.512A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.568A pdb=" N ASP B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 255 through 269 removed outlier: 3.842A pdb=" N LYS B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 327 through 347 removed outlier: 3.589A pdb=" N THR B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.628A pdb=" N ALA B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.769A pdb=" N PHE C 28 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 52 through 63 Processing helix chain 'C' and resid 66 through 77 removed outlier: 4.001A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 119 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 143 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 203 through 217 Processing helix chain 'C' and resid 229 through 242 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 268 Processing helix chain 'C' and resid 286 through 301 Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.640A pdb=" N ILE C 315 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.653A pdb=" N TRP C 361 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 375 through 381 removed outlier: 3.957A pdb=" N ALA C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.607A pdb=" N LYS D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.502A pdb=" N TYR D 27 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE D 28 " --> pdb=" O SER D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 31 through 48 removed outlier: 3.671A pdb=" N PHE D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 86 through 118 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.936A pdb=" N ILE D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 327 through 347 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 375 through 380 removed outlier: 4.004A pdb=" N ALA D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.594A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.560A pdb=" N PHE E 28 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 66 through 79 Processing helix chain 'E' and resid 86 through 118 Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.534A pdb=" N ALA E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 166 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.587A pdb=" N ASP E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 286 through 301 Processing helix chain 'E' and resid 327 through 347 removed outlier: 3.842A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 390 through 397 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.760A pdb=" N ASN F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 66 through 80 Processing helix chain 'F' and resid 88 through 118 removed outlier: 3.903A pdb=" N LYS F 92 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 133 through 142 removed outlier: 3.660A pdb=" N LEU F 142 " --> pdb=" O MET F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 229 through 243 Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.706A pdb=" N LYS F 269 " --> pdb=" O LYS F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 302 Processing helix chain 'F' and resid 327 through 347 Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'H' and resid 4 through 18 removed outlier: 3.547A pdb=" N ASP H 8 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG H 14 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS H 18 " --> pdb=" O ARG H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 82 through 96 removed outlier: 3.858A pdb=" N GLU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 146 through 152 removed outlier: 4.001A pdb=" N LYS H 151 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 167 Processing helix chain 'H' and resid 221 through 225 Processing helix chain 'H' and resid 237 through 242 removed outlier: 3.606A pdb=" N PHE H 241 " --> pdb=" O ASP H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 287 Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.606A pdb=" N GLY H 312 " --> pdb=" O ILE H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 325 removed outlier: 3.738A pdb=" N ILE H 318 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS H 323 " --> pdb=" O MET H 319 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN H 324 " --> pdb=" O GLU H 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 6.565A pdb=" N VAL B 221 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LYS B 278 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B 223 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 222 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 405 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.511A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 192 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LEU A 385 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 194 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL A 387 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET A 196 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A 191 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR A 352 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN A 193 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ALA A 354 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 195 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 222 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 221 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A 278 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR A 223 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.614A pdb=" N VAL C 221 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS C 278 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR C 223 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN C 220 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE C 309 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 222 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 383 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 422 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.510A pdb=" N VAL D 221 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LYS D 278 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR D 223 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE D 309 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 222 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.876A pdb=" N ALA E 353 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E 354 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU E 192 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU E 385 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 194 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL E 387 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET E 196 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET E 384 " --> pdb=" O ILE E 404 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AB3, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.037A pdb=" N THR D 191 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR D 352 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU D 192 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU D 385 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D 194 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL D 387 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET D 196 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N MET D 384 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AB5, first strand: chain 'F' and resid 349 through 352 removed outlier: 3.708A pdb=" N PHE F 383 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 275 through 279 removed outlier: 6.325A pdb=" N LEU F 222 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 419 through 422 Processing sheet with id=AB8, first strand: chain 'H' and resid 23 through 26 Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 126 removed outlier: 3.753A pdb=" N SER H 193 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 219 through 220 removed outlier: 3.536A pdb=" N ILE H 248 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL H 230 " --> pdb=" O VAL H 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 290 through 292 removed outlier: 3.508A pdb=" N ALA H 327 " --> pdb=" O VAL H 291 " (cutoff:3.500A) 1158 hydrogen bonds defined for protein. 3303 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: 8.91 Time building geometry restraints manager: 10.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7549 1.35 - 1.50: 6411 1.50 - 1.65: 10008 1.65 - 1.80: 105 1.80 - 1.95: 124 Bond restraints: 24197 Sorted by residual: bond pdb=" CE1 HIS D 87 " pdb=" NE2 HIS D 87 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.48e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.24e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.039 1.18e-02 7.18e+03 1.12e+01 bond pdb=" N TRP D 20 " pdb=" CA TRP D 20 " ideal model delta sigma weight residual 1.462 1.492 -0.030 9.50e-03 1.11e+04 9.92e+00 bond pdb=" N TRP E 20 " pdb=" CA TRP E 20 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.04e-02 9.25e+03 9.69e+00 ... (remaining 24192 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.13: 614 106.13 - 113.17: 13252 113.17 - 120.21: 8750 120.21 - 127.25: 9906 127.25 - 134.29: 285 Bond angle restraints: 32807 Sorted by residual: angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.58 -12.46 3.00e+00 1.11e-01 1.73e+01 angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 112.57 108.05 4.52 1.13e+00 7.83e-01 1.60e+01 angle pdb=" N GLU H 92 " pdb=" CA GLU H 92 " pdb=" C GLU H 92 " ideal model delta sigma weight residual 111.71 107.18 4.53 1.15e+00 7.56e-01 1.55e+01 angle pdb=" CA PHE D 383 " pdb=" CB PHE D 383 " pdb=" CG PHE D 383 " ideal model delta sigma weight residual 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.55e+01 angle pdb=" C GLY F 151 " pdb=" N HIS F 152 " pdb=" CA HIS F 152 " ideal model delta sigma weight residual 122.30 117.07 5.23 1.35e+00 5.49e-01 1.50e+01 ... (remaining 32802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 14414 35.65 - 71.31: 202 71.31 - 106.96: 10 106.96 - 142.62: 1 142.62 - 178.27: 4 Dihedral angle restraints: 14631 sinusoidal: 6069 harmonic: 8562 Sorted by residual: dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -112.82 -178.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 106.43 -174.16 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -88.62 157.53 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 14628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2650 0.044 - 0.088: 645 0.088 - 0.132: 288 0.132 - 0.176: 48 0.176 - 0.220: 16 Chirality restraints: 3647 Sorted by residual: chirality pdb=" CA ILE H 93 " pdb=" N ILE H 93 " pdb=" C ILE H 93 " pdb=" CB ILE H 93 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL A 150 " pdb=" N VAL A 150 " pdb=" C VAL A 150 " pdb=" CB VAL A 150 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ARG A 124 " pdb=" N ARG A 124 " pdb=" C ARG A 124 " pdb=" CB ARG A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3644 not shown) Planarity restraints: 4071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 266 " 0.018 2.00e-02 2.50e+03 2.32e-02 1.35e+01 pdb=" CG TRP H 266 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP H 266 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP H 266 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 266 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 266 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 266 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 266 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 266 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP H 266 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 373 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLU A 373 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 373 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 374 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 145 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C SER B 145 " 0.039 2.00e-02 2.50e+03 pdb=" O SER B 145 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 146 " -0.013 2.00e-02 2.50e+03 ... (remaining 4068 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 113 2.47 - 3.07: 16357 3.07 - 3.68: 36394 3.68 - 4.29: 55354 4.29 - 4.90: 90583 Nonbonded interactions: 198801 Sorted by model distance: nonbonded pdb=" O1B AGS C 501 " pdb="MG MG C 502 " model vdw 1.856 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.972 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.979 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.985 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 ... (remaining 198796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 65.710 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.120 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 0.051 24197 Z= 0.295 Angle : 0.682 12.461 32807 Z= 0.446 Chirality : 0.049 0.220 3647 Planarity : 0.004 0.075 4071 Dihedral : 12.486 178.275 9101 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.78 % Allowed : 7.25 % Favored : 90.96 % 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: 0.23 (0.16), residues: 2898 helix: 1.29 (0.14), residues: 1435 sheet: -0.35 (0.27), residues: 407 loop : -1.20 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP H 266 HIS 0.008 0.001 HIS B 152 PHE 0.022 0.002 PHE D 383 TYR 0.014 0.001 TYR E 329 ARG 0.004 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 722 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7054 (m) cc_final: 0.6730 (t) REVERT: A 327 ASN cc_start: 0.3766 (OUTLIER) cc_final: 0.3367 (p0) REVERT: A 347 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7665 (mm-30) REVERT: A 368 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.5816 (ttm) REVERT: A 369 SER cc_start: 0.5907 (m) cc_final: 0.5494 (p) REVERT: B 48 HIS cc_start: 0.7610 (m90) cc_final: 0.7105 (m90) REVERT: B 96 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8100 (mtpp) REVERT: B 267 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7587 (ttp-170) REVERT: B 422 GLN cc_start: 0.6749 (mt0) cc_final: 0.6413 (mm-40) REVERT: C 128 MET cc_start: 0.5747 (tpp) cc_final: 0.5430 (mmt) REVERT: C 323 VAL cc_start: 0.7577 (t) cc_final: 0.7043 (t) REVERT: D 26 GLU cc_start: 0.7746 (mp0) cc_final: 0.7447 (mm-30) REVERT: D 265 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7465 (tmmt) REVERT: E 109 LYS cc_start: 0.7506 (tptt) cc_final: 0.7221 (ttmt) REVERT: E 338 GLU cc_start: 0.6474 (mt-10) cc_final: 0.6216 (mp0) REVERT: E 380 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7935 (p) REVERT: F 128 MET cc_start: 0.6055 (ttt) cc_final: 0.5835 (ttm) REVERT: F 156 ASP cc_start: 0.7667 (t0) cc_final: 0.7429 (t0) REVERT: F 167 ASN cc_start: 0.6020 (OUTLIER) cc_final: 0.4854 (m-40) REVERT: F 213 ASP cc_start: 0.7586 (m-30) cc_final: 0.7311 (m-30) REVERT: F 276 ILE cc_start: 0.8836 (mt) cc_final: 0.8628 (tt) REVERT: F 345 GLU cc_start: 0.7727 (tt0) cc_final: 0.7486 (tt0) REVERT: F 355 GLN cc_start: 0.6770 (tt0) cc_final: 0.6483 (pm20) REVERT: F 399 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6921 (tp40) REVERT: F 423 LYS cc_start: 0.8029 (mttm) cc_final: 0.7779 (mttp) REVERT: H 161 LYS cc_start: 0.4172 (tmmt) cc_final: 0.3865 (mttt) REVERT: H 283 LYS cc_start: 0.7693 (tttt) cc_final: 0.7449 (mtmt) REVERT: H 294 TRP cc_start: 0.7286 (m100) cc_final: 0.7085 (m100) REVERT: H 305 ASN cc_start: 0.6222 (t0) cc_final: 0.5935 (t0) REVERT: H 307 MET cc_start: 0.6672 (mtt) cc_final: 0.6405 (mtt) outliers start: 45 outliers final: 4 residues processed: 750 average time/residue: 0.4290 time to fit residues: 472.7113 Evaluate side-chains 381 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 372 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 228 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 264 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 140 GLN A 167 ASN A 288 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN B 253 HIS ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS C 114 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 288 ASN C 295 ASN D 48 HIS D 200 ASN D 403 GLN E 114 GLN F 8 HIS F 62 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN H 317 GLN ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24197 Z= 0.222 Angle : 0.554 8.325 32807 Z= 0.301 Chirality : 0.042 0.238 3647 Planarity : 0.004 0.051 4071 Dihedral : 10.922 175.843 3415 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.22 % Allowed : 11.65 % Favored : 86.13 % 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: 0.44 (0.16), residues: 2898 helix: 1.46 (0.14), residues: 1458 sheet: -0.27 (0.27), residues: 417 loop : -1.14 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 266 HIS 0.012 0.001 HIS B 87 PHE 0.014 0.002 PHE D 65 TYR 0.018 0.001 TYR H 213 ARG 0.006 0.001 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 391 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8456 (mmt) cc_final: 0.8222 (mmt) REVERT: A 263 MET cc_start: 0.7160 (mmm) cc_final: 0.6869 (mmm) REVERT: A 266 TRP cc_start: 0.7439 (m100) cc_final: 0.7234 (m100) REVERT: A 369 SER cc_start: 0.6109 (m) cc_final: 0.5714 (p) REVERT: B 48 HIS cc_start: 0.7644 (m90) cc_final: 0.7325 (m90) REVERT: B 248 ASP cc_start: 0.7337 (m-30) cc_final: 0.7112 (m-30) REVERT: B 333 LYS cc_start: 0.7776 (ttpp) cc_final: 0.7411 (ttmt) REVERT: B 422 GLN cc_start: 0.6885 (mt0) cc_final: 0.6467 (mm-40) REVERT: C 69 GLU cc_start: 0.7016 (pt0) cc_final: 0.6471 (mm-30) REVERT: D 26 GLU cc_start: 0.7927 (mp0) cc_final: 0.7667 (mm-30) REVERT: D 247 ASP cc_start: 0.7572 (m-30) cc_final: 0.7089 (t70) REVERT: E 103 MET cc_start: 0.8356 (mmm) cc_final: 0.8096 (mmt) REVERT: E 118 GLU cc_start: 0.7343 (pp20) cc_final: 0.7072 (mp0) REVERT: E 338 GLU cc_start: 0.6618 (mt-10) cc_final: 0.6184 (mp0) REVERT: F 156 ASP cc_start: 0.7964 (t0) cc_final: 0.7694 (t0) REVERT: F 167 ASN cc_start: 0.6290 (OUTLIER) cc_final: 0.5210 (m110) REVERT: F 226 MET cc_start: 0.8330 (mmm) cc_final: 0.7678 (mmt) REVERT: F 227 GLU cc_start: 0.6877 (pt0) cc_final: 0.6502 (tt0) REVERT: F 373 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6771 (mm-30) REVERT: F 399 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7024 (tp40) REVERT: H 161 LYS cc_start: 0.3905 (tmmt) cc_final: 0.3586 (mmtt) REVERT: H 292 MET cc_start: 0.5945 (tpp) cc_final: 0.5183 (tpt) REVERT: H 328 GLN cc_start: 0.6764 (pt0) cc_final: 0.6487 (pt0) outliers start: 56 outliers final: 29 residues processed: 433 average time/residue: 0.3729 time to fit residues: 245.8413 Evaluate side-chains 342 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 311 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 304 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: 52.1731 > 50: distance: 57 - 116: 3.596 distance: 69 - 99: 21.092 distance: 97 - 98: 3.482 distance: 98 - 99: 19.128 distance: 98 - 105: 5.603 distance: 101 - 102: 3.865 distance: 103 - 104: 7.152 distance: 105 - 228: 5.325 distance: 106 - 107: 5.549 distance: 107 - 108: 4.064 distance: 107 - 113: 5.373 distance: 108 - 225: 10.906 distance: 109 - 110: 3.650 distance: 110 - 111: 6.456 distance: 110 - 112: 4.485 distance: 113 - 114: 3.491 distance: 114 - 117: 3.106 distance: 117 - 118: 3.170 distance: 118 - 119: 5.468 distance: 119 - 120: 9.407 distance: 120 - 121: 4.532 distance: 121 - 122: 10.140 distance: 121 - 123: 6.235 distance: 124 - 125: 3.486 distance: 124 - 210: 6.245 distance: 125 - 128: 3.238 distance: 126 - 135: 3.039 distance: 127 - 207: 4.273 distance: 135 - 136: 8.194 distance: 136 - 137: 10.258 distance: 136 - 139: 6.427 distance: 137 - 138: 6.667 distance: 137 - 146: 6.601 distance: 139 - 140: 4.378 distance: 140 - 141: 8.140 distance: 141 - 142: 7.467 distance: 142 - 143: 8.926 distance: 143 - 144: 6.361 distance: 143 - 145: 7.076 distance: 146 - 147: 9.588 distance: 147 - 148: 9.085 distance: 147 - 150: 14.904 distance: 148 - 149: 11.498 distance: 148 - 152: 5.372 distance: 150 - 151: 17.693 distance: 152 - 158: 8.644 distance: 153 - 154: 17.477 distance: 153 - 156: 19.763 distance: 154 - 155: 25.727 distance: 154 - 159: 11.817 distance: 156 - 157: 12.900 distance: 157 - 158: 11.558 distance: 159 - 160: 15.192 distance: 160 - 161: 9.281 distance: 160 - 163: 20.461 distance: 161 - 162: 8.614 distance: 161 - 166: 6.141 distance: 163 - 164: 4.860 distance: 163 - 165: 7.859 distance: 166 - 167: 8.506 distance: 167 - 168: 4.016 distance: 167 - 170: 12.600 distance: 168 - 169: 18.666 distance: 168 - 172: 12.464 distance: 170 - 171: 8.514 distance: 172 - 173: 5.684 distance: 173 - 174: 5.225 distance: 174 - 175: 9.993 distance: 174 - 176: 5.755