Starting phenix.real_space_refine on Thu Mar 14 20:15:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arj_11884/03_2024/7arj_11884_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arj_11884/03_2024/7arj_11884.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/7arj_11884/03_2024/7arj_11884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arj_11884/03_2024/7arj_11884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arj_11884/03_2024/7arj_11884_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arj_11884/03_2024/7arj_11884_updated.pdb" } 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 56 atoms to isotropic. 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 6 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 6112 2.51 5 N 1684 2.21 5 O 1745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C ASP 227": "OD1" <-> "OD2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C ASP 251": "OD1" <-> "OD2" Residue "C PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E GLU 67": "OE1" <-> "OE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 264": "OD1" <-> "OD2" Residue "E ASP 297": "OD1" <-> "OD2" Residue "E ASP 312": "OD1" <-> "OD2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 151": "NH1" <-> "NH2" Residue "F ASP 170": "OD1" <-> "OD2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D ASP 177": "OD1" <-> "OD2" Residue "D ASP 182": "OD1" <-> "OD2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 226": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9601 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2965 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3159 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain: "F" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1588 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 8, 'TRANS': 216} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Chain: "D" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1696 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 217} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "V" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 73 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 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, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.51, per 1000 atoms: 0.57 Number of scatterers: 9601 At special positions: 0 Unit cell: (83.148, 91.26, 153.114, 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 52 16.00 P 6 15.00 Mg 2 11.99 O 1745 8.00 N 1684 7.00 C 6112 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.39 Conformation dependent library (CDL) restraints added in 1.8 seconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 9 sheets defined 33.4% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'C' and resid 23 through 27 removed outlier: 4.442A pdb=" N SER C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 27' Processing helix chain 'C' and resid 29 through 56 removed outlier: 3.659A pdb=" N ILE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR C 43 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 256 through 292 removed outlier: 3.924A pdb=" N VAL C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 removed outlier: 3.705A pdb=" N ILE C 299 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 313 through 317 removed outlier: 4.064A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 317' Processing helix chain 'C' and resid 320 through 338 removed outlier: 3.538A pdb=" N ALA C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 388 removed outlier: 4.026A pdb=" N ILE C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 379 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Proline residue: C 383 - end of helix removed outlier: 3.625A pdb=" N ALA C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 16 Processing helix chain 'E' and resid 22 through 58 removed outlier: 4.028A pdb=" N SER E 27 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 30 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE E 32 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLY E 33 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE E 34 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU E 36 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY E 37 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA E 39 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL E 40 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE E 42 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 43 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY E 44 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 45 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER E 46 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA E 47 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN E 49 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 52 " --> pdb=" O ASN E 49 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 53 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU E 54 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU E 55 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN E 56 " --> pdb=" O ARG E 53 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN E 57 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG E 58 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 83 No H-bonds generated for 'chain 'E' and resid 80 through 83' Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 152 through 158 removed outlier: 3.505A pdb=" N ASP E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 214 removed outlier: 3.537A pdb=" N GLN E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 255 through 258 No H-bonds generated for 'chain 'E' and resid 255 through 258' Processing helix chain 'E' and resid 261 through 267 removed outlier: 3.504A pdb=" N ILE E 265 " --> pdb=" O MET E 261 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET E 267 " --> pdb=" O ARG E 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 261 through 267' Processing helix chain 'E' and resid 272 through 308 removed outlier: 3.532A pdb=" N VAL E 277 " --> pdb=" O TYR E 273 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLY E 300 " --> pdb=" O LYS E 296 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ASP E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL E 304 " --> pdb=" O GLY E 300 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 343 removed outlier: 3.604A pdb=" N ILE E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE E 319 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E 320 " --> pdb=" O ARG E 316 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS E 333 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 356 removed outlier: 3.719A pdb=" N GLU E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 355 " --> pdb=" O TRP E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 394 Processing helix chain 'E' and resid 397 through 401 Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 78 through 87 removed outlier: 3.545A pdb=" N GLN F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.923A pdb=" N VAL F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 104 through 108' Processing helix chain 'F' and resid 110 through 114 Processing helix chain 'F' and resid 122 through 133 removed outlier: 3.516A pdb=" N LEU F 127 " --> pdb=" O ASN F 123 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET F 129 " --> pdb=" O ARG F 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 159 removed outlier: 3.823A pdb=" N GLN F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 183 removed outlier: 3.594A pdb=" N SER F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'D' and resid 48 through 54 removed outlier: 3.844A pdb=" N LEU D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 87 No H-bonds generated for 'chain 'D' and resid 84 through 87' Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.987A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 108' Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.767A pdb=" N ILE D 114 " --> pdb=" O MET D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 110 through 114' Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing sheet with id= A, first strand: chain 'C' and resid 245 through 247 removed outlier: 4.687A pdb=" N ALA C 66 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 224 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP C 222 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 221 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 96 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 180 through 185 removed outlier: 4.006A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 166 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 164 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY C 99 " --> pdb=" O MET C 114 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 112 " --> pdb=" O VAL C 101 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 250 through 253 removed outlier: 3.561A pdb=" N LYS E 252 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 67 " --> pdb=" O LYS E 252 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY E 66 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS E 227 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA E 93 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 115 through 118 removed outlier: 6.634A pdb=" N ALA E 204 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL E 118 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE E 206 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 165 through 170 removed outlier: 3.909A pdb=" N ILE E 168 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL E 185 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE E 170 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 89 through 92 removed outlier: 6.804A pdb=" N LEU F 166 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE F 92 " --> pdb=" O LEU F 166 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU F 168 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA F 198 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA F 169 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU F 200 " --> pdb=" O ALA F 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.381A pdb=" N MET D 38 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N THR D 203 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE D 40 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU D 216 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.949A pdb=" N LEU D 166 " --> pdb=" O GLY D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'D' and resid 13 through 16 removed outlier: 3.736A pdb=" N LEU D 25 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TYR D 15 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP D 23 " --> pdb=" O TYR D 15 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 537 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3105 1.34 - 1.46: 1119 1.46 - 1.57: 5423 1.57 - 1.69: 11 1.69 - 1.81: 98 Bond restraints: 9756 Sorted by residual: bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C16 Z41 V 101 " pdb=" O2 Z41 V 101 " ideal model delta sigma weight residual 1.332 1.455 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C19 Z41 V 101 " pdb=" O3 Z41 V 101 " ideal model delta sigma weight residual 1.333 1.454 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.68e+01 ... (remaining 9751 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.33: 292 106.33 - 113.24: 5398 113.24 - 120.14: 3476 120.14 - 127.04: 3951 127.04 - 133.94: 108 Bond angle restraints: 13225 Sorted by residual: angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 109.77 17.18 3.00e+00 1.11e-01 3.28e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 109.82 17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" C PRO F 61 " pdb=" N THR F 62 " pdb=" CA THR F 62 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C ARG D 219 " pdb=" N ASP D 220 " pdb=" CA ASP D 220 " ideal model delta sigma weight residual 121.54 128.66 -7.12 1.91e+00 2.74e-01 1.39e+01 angle pdb=" O1B ANP D 401 " pdb=" PB ANP D 401 " pdb=" O2B ANP D 401 " ideal model delta sigma weight residual 120.08 109.91 10.17 3.00e+00 1.11e-01 1.15e+01 ... (remaining 13220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.56: 5478 18.56 - 37.13: 355 37.13 - 55.69: 83 55.69 - 74.25: 18 74.25 - 92.82: 4 Dihedral angle restraints: 5938 sinusoidal: 2350 harmonic: 3588 Sorted by residual: dihedral pdb=" CA LEU E 195 " pdb=" C LEU E 195 " pdb=" N SER E 196 " pdb=" CA SER E 196 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ASP C 227 " pdb=" CB ASP C 227 " pdb=" CG ASP C 227 " pdb=" OD1 ASP C 227 " ideal model delta sinusoidal sigma weight residual -30.00 -88.20 58.20 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" O1B ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PB ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sinusoidal sigma weight residual 35.15 -57.67 92.82 1 3.00e+01 1.11e-03 1.12e+01 ... (remaining 5935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1239 0.054 - 0.109: 268 0.109 - 0.163: 44 0.163 - 0.217: 4 0.217 - 0.271: 2 Chirality restraints: 1557 Sorted by residual: chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA THR F 62 " pdb=" N THR F 62 " pdb=" C THR F 62 " pdb=" CB THR F 62 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 1554 not shown) Planarity restraints: 1679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 178 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO C 179 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 306 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO C 307 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 184 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C ILE D 184 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE D 184 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE D 185 " -0.013 2.00e-02 2.50e+03 ... (remaining 1676 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2966 2.83 - 3.35: 7609 3.35 - 3.86: 14851 3.86 - 4.38: 16799 4.38 - 4.90: 28889 Nonbonded interactions: 71114 Sorted by model distance: nonbonded pdb=" OG SER F 49 " pdb=" O1A ANP F 401 " model vdw 2.312 2.440 nonbonded pdb=" O TYR E 382 " pdb=" OG1 THR E 386 " model vdw 2.342 2.440 nonbonded pdb=" O SER E 412 " pdb=" OG SER E 412 " model vdw 2.362 2.440 nonbonded pdb=" O SER E 27 " pdb=" OG1 THR E 31 " model vdw 2.363 2.440 nonbonded pdb=" OG1 THR E 245 " pdb=" OD1 ASN E 246 " model vdw 2.368 2.440 ... (remaining 71109 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 'D' and (resid 4 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or (resid 18 through 21 and (name N or nam \ e CA or name C or name O or name CB )) or resid 22 or (resid 23 and (name N or n \ ame CA or name C or name O or name CB )) or resid 24 through 35 or (resid 36 and \ (name N or name CA or name C or name O or name CB )) or resid 37 through 93 or \ (resid 94 through 95 and (name N or name CA or name C or name O or name CB )) or \ resid 96 through 117 or (resid 118 and (name N or name CA or name C or name O o \ r name CB )) or resid 119 through 120 or (resid 121 and (name N or name CA or na \ me C or name O or name CB )) or resid 122 through 130 or (resid 131 through 132 \ and (name N or name CA or name C or name O or name CB )) or resid 133 through 13 \ 5 or (resid 136 and (name N or name CA or name C or name O or name CB )) or resi \ d 137 through 152 or (resid 153 and (name N or name CA or name C or name O or na \ me CB )) or resid 154 through 174 or (resid 175 and (name N or name CA or name C \ or name O or name CB )) or resid 176 or (resid 177 through 182 and (name N or n \ ame CA or name C or name O or name CB )) or resid 183 through 186 or (resid 187 \ and (name N or name CA or name C or name O or name CB )) or resid 188 through 19 \ 3 or (resid 194 through 195 and (name N or name CA or name C or name O or name C \ B )) or resid 196 through 209 or (resid 210 and (name N or name CA or name C or \ name O or name CB )) or resid 211 through 216 or (resid 217 and (name N or name \ CA or name C or name O or name CB )) or resid 218 or (resid 219 through 220 and \ (name N or name CA or name C or name O or name CB )) or resid 221 or (resid 222 \ through 228 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 1 through 402)) selection = (chain 'F' and (resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 or (resid 13 through 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 61 or (resid 62 and (n \ ame N or name CA or name C or name O or name CB )) or resid 63 through 228 or re \ sid 401 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 3.410 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.910 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.005 0.141 9756 Z= 0.295 Angle : 0.802 17.179 13225 Z= 0.367 Chirality : 0.047 0.271 1557 Planarity : 0.005 0.071 1679 Dihedral : 13.517 92.817 3628 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.10 % Allowed : 5.24 % Favored : 94.66 % 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: -5.75 (0.16), residues: 1250 helix: -5.01 (0.05), residues: 430 sheet: -2.33 (0.44), residues: 122 loop : -3.37 (0.17), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 321 HIS 0.001 0.000 HIS F 137 PHE 0.012 0.001 PHE C 190 TYR 0.008 0.001 TYR C 199 ARG 0.002 0.000 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 1.103 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: E 48 MET cc_start: 0.8344 (mmt) cc_final: 0.7867 (mmt) REVERT: E 97 TYR cc_start: 0.7953 (p90) cc_final: 0.7387 (p90) REVERT: E 337 ILE cc_start: 0.8057 (tt) cc_final: 0.7794 (tp) REVERT: F 69 ASN cc_start: 0.8785 (t0) cc_final: 0.8518 (t0) REVERT: F 140 ASN cc_start: 0.8811 (m110) cc_final: 0.8552 (m-40) REVERT: F 200 LEU cc_start: 0.7106 (pp) cc_final: 0.6837 (pp) REVERT: D 10 ASN cc_start: 0.6555 (t0) cc_final: 0.6347 (t0) REVERT: D 212 MET cc_start: 0.2214 (mmt) cc_final: 0.1865 (ptm) REVERT: D 218 MET cc_start: 0.7525 (tpp) cc_final: 0.7144 (tpt) outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.2471 time to fit residues: 102.1679 Evaluate side-chains 224 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 ASN C 309 GLN C 341 ASN E 56 ASN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS E 286 ASN F 53 HIS ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN F 163 ASN F 192 ASN D 71 GLN D 97 HIS D 140 ASN D 163 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9756 Z= 0.172 Angle : 0.568 7.342 13225 Z= 0.272 Chirality : 0.042 0.189 1557 Planarity : 0.004 0.044 1679 Dihedral : 8.975 133.672 1456 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.01 % Allowed : 15.31 % Favored : 82.68 % 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: -4.26 (0.18), residues: 1250 helix: -3.32 (0.16), residues: 440 sheet: -1.85 (0.43), residues: 143 loop : -2.72 (0.20), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.003 0.001 HIS E 84 PHE 0.010 0.001 PHE E 329 TYR 0.009 0.001 TYR E 258 ARG 0.003 0.000 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 240 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 281 ASN cc_start: 0.8537 (t0) cc_final: 0.8335 (t0) REVERT: C 363 LEU cc_start: 0.8323 (tp) cc_final: 0.8041 (tt) REVERT: E 337 ILE cc_start: 0.8817 (tt) cc_final: 0.8528 (tp) REVERT: E 346 THR cc_start: 0.6396 (OUTLIER) cc_final: 0.6048 (p) REVERT: E 392 LEU cc_start: 0.8139 (tt) cc_final: 0.7807 (mt) REVERT: F 34 GLU cc_start: 0.6667 (mp0) cc_final: 0.6389 (mp0) REVERT: F 83 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7790 (mt-10) REVERT: F 141 HIS cc_start: 0.7503 (m-70) cc_final: 0.7202 (m-70) REVERT: F 192 ASN cc_start: 0.7150 (m-40) cc_final: 0.6840 (t0) REVERT: D 10 ASN cc_start: 0.6780 (t0) cc_final: 0.6576 (t0) REVERT: D 152 GLN cc_start: 0.7060 (tp40) cc_final: 0.6521 (pm20) REVERT: D 171 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6975 (tm-30) REVERT: D 212 MET cc_start: 0.2267 (mmt) cc_final: 0.2006 (ptm) REVERT: D 220 ASP cc_start: 0.8546 (p0) cc_final: 0.8229 (p0) outliers start: 20 outliers final: 12 residues processed: 251 average time/residue: 0.2222 time to fit residues: 75.9467 Evaluate side-chains 226 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 213 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 41 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 100 optimal weight: 20.0000 chunk 111 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS C 161 GLN C 309 GLN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 HIS ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9756 Z= 0.149 Angle : 0.521 6.835 13225 Z= 0.249 Chirality : 0.041 0.140 1557 Planarity : 0.003 0.040 1679 Dihedral : 8.551 135.906 1456 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.32 % Allowed : 15.91 % Favored : 80.77 % 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: -3.11 (0.21), residues: 1250 helix: -1.88 (0.21), residues: 454 sheet: -1.41 (0.46), residues: 137 loop : -2.35 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 138 HIS 0.008 0.001 HIS E 84 PHE 0.015 0.001 PHE F 68 TYR 0.016 0.001 TYR C 142 ARG 0.009 0.000 ARG E 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 230 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 363 LEU cc_start: 0.8361 (tp) cc_final: 0.8063 (tt) REVERT: E 337 ILE cc_start: 0.9048 (tt) cc_final: 0.8748 (tp) REVERT: F 59 ASP cc_start: 0.8108 (t0) cc_final: 0.7791 (t0) REVERT: F 83 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7923 (mt-10) REVERT: F 141 HIS cc_start: 0.7517 (m-70) cc_final: 0.7168 (m-70) REVERT: F 156 ILE cc_start: 0.9081 (mt) cc_final: 0.8759 (mm) REVERT: D 10 ASN cc_start: 0.6798 (t0) cc_final: 0.6570 (t0) REVERT: D 136 ASP cc_start: 0.7487 (t0) cc_final: 0.7070 (m-30) REVERT: D 171 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6895 (tm-30) REVERT: D 220 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7959 (p0) outliers start: 33 outliers final: 20 residues processed: 247 average time/residue: 0.2204 time to fit residues: 74.4619 Evaluate side-chains 229 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 220 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS C 317 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS E 114 GLN E 134 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9756 Z= 0.271 Angle : 0.611 7.774 13225 Z= 0.300 Chirality : 0.045 0.190 1557 Planarity : 0.003 0.034 1679 Dihedral : 8.840 132.852 1456 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.42 % Allowed : 17.72 % Favored : 78.85 % 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: -2.66 (0.22), residues: 1250 helix: -1.38 (0.22), residues: 479 sheet: -1.25 (0.48), residues: 128 loop : -2.17 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 165 HIS 0.004 0.001 HIS E 358 PHE 0.014 0.002 PHE F 68 TYR 0.013 0.001 TYR E 322 ARG 0.006 0.001 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 204 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.7441 (tp30) cc_final: 0.7053 (tp30) REVERT: C 310 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8698 (tt) REVERT: E 350 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: F 59 ASP cc_start: 0.8161 (t0) cc_final: 0.7689 (t0) REVERT: F 83 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7907 (mt-10) REVERT: F 141 HIS cc_start: 0.7775 (m-70) cc_final: 0.7462 (m-70) REVERT: F 191 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8198 (mm) REVERT: D 10 ASN cc_start: 0.7051 (t0) cc_final: 0.6793 (t0) REVERT: D 14 ARG cc_start: 0.7139 (ttp80) cc_final: 0.6895 (ttp80) REVERT: D 30 PHE cc_start: 0.8069 (t80) cc_final: 0.7820 (t80) REVERT: D 171 GLU cc_start: 0.7454 (tm-30) cc_final: 0.6937 (tm-30) outliers start: 34 outliers final: 17 residues processed: 225 average time/residue: 0.2292 time to fit residues: 69.8727 Evaluate side-chains 204 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1309 > 50: distance: 41 - 46: 21.843 distance: 46 - 47: 9.691 distance: 47 - 48: 13.381 distance: 47 - 50: 14.691 distance: 48 - 49: 21.973 distance: 48 - 51: 20.663 distance: 51 - 52: 21.555 distance: 52 - 53: 10.172 distance: 52 - 55: 19.471 distance: 53 - 54: 20.460 distance: 53 - 57: 10.948 distance: 55 - 56: 32.118 distance: 57 - 58: 10.401 distance: 58 - 59: 15.772 distance: 59 - 60: 11.032 distance: 59 - 61: 20.146 distance: 61 - 62: 12.228 distance: 62 - 63: 10.998 distance: 62 - 65: 36.425 distance: 63 - 64: 18.952 distance: 63 - 66: 40.449 distance: 66 - 67: 28.682 distance: 67 - 68: 26.366 distance: 67 - 70: 18.410 distance: 68 - 69: 43.848 distance: 68 - 73: 16.015 distance: 70 - 71: 32.978 distance: 70 - 72: 37.113 distance: 73 - 74: 24.783 distance: 74 - 75: 32.957 distance: 74 - 77: 17.038 distance: 75 - 76: 27.884 distance: 75 - 81: 10.097 distance: 77 - 78: 31.610 distance: 77 - 79: 30.953 distance: 78 - 80: 36.874 distance: 81 - 82: 7.346 distance: 82 - 83: 5.682 distance: 82 - 85: 10.010 distance: 83 - 84: 22.439 distance: 83 - 92: 12.788 distance: 85 - 86: 6.331 distance: 86 - 87: 4.395 distance: 87 - 89: 4.818 distance: 89 - 91: 3.354 distance: 92 - 93: 22.119 distance: 93 - 94: 29.109 distance: 93 - 96: 28.288 distance: 94 - 95: 40.831 distance: 94 - 100: 19.679 distance: 96 - 97: 8.906 distance: 97 - 98: 10.606 distance: 97 - 99: 14.915 distance: 100 - 101: 39.859 distance: 101 - 102: 22.103 distance: 102 - 103: 48.323 distance: 102 - 104: 32.190 distance: 104 - 105: 15.463 distance: 105 - 106: 16.455 distance: 105 - 108: 9.311 distance: 106 - 107: 17.867 distance: 106 - 113: 5.597 distance: 108 - 109: 12.345 distance: 109 - 110: 21.970 distance: 110 - 111: 10.016 distance: 110 - 112: 8.085