Starting phenix.real_space_refine on Tue Aug 6 19:06:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxn_27770/08_2024/8dxn_27770.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxn_27770/08_2024/8dxn_27770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxn_27770/08_2024/8dxn_27770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxn_27770/08_2024/8dxn_27770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxn_27770/08_2024/8dxn_27770.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxn_27770/08_2024/8dxn_27770.cif" } resolution = 3.4 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= -0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 11561 2.51 5 N 2760 2.21 5 O 3031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 348": "OE1" <-> "OE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "E PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 104": "OD1" <-> "OD2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 296": "OD1" <-> "OD2" Residue "F PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 348": "OE1" <-> "OE2" Residue "F PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 296": "OD1" <-> "OD2" Residue "G TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17499 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2481 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 7, 'TRANS': 290} Chain breaks: 2 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2501 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2507 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Chain: "D" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2497 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "E" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2507 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Chain: "F" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2516 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 7, 'TRANS': 294} Chain breaks: 2 Chain: "G" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2490 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain breaks: 2 Time building chain proxies: 9.65, per 1000 atoms: 0.55 Number of scatterers: 17499 At special positions: 0 Unit cell: (119.9, 117.7, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 3031 8.00 N 2760 7.00 C 11561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 293 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 115 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 293 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 308 " distance=2.03 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 293 " distance=2.03 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: 6.25 Conformation dependent library (CDL) restraints added in 3.0 seconds 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4062 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 7 sheets defined 72.3% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 106 through 119 removed outlier: 3.738A pdb=" N GLU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.585A pdb=" N LYS A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 144 Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.860A pdb=" N ASP A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.906A pdb=" N THR A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 254 removed outlier: 3.945A pdb=" N GLU A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 283 removed outlier: 3.601A pdb=" N VAL A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 342 removed outlier: 3.652A pdb=" N PHE A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 removed outlier: 3.767A pdb=" N GLN A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 removed outlier: 4.215A pdb=" N GLN A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 3.690A pdb=" N PHE A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 405 removed outlier: 3.916A pdb=" N GLU A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 4.052A pdb=" N VAL B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 49 removed outlier: 5.135A pdb=" N ASP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.779A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.700A pdb=" N LYS B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 126' Processing helix chain 'B' and resid 126 through 143 removed outlier: 3.519A pdb=" N ASN B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.787A pdb=" N THR B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Processing helix chain 'B' and resid 259 through 283 Processing helix chain 'B' and resid 314 through 341 removed outlier: 3.955A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 367 through 378 removed outlier: 3.679A pdb=" N ALA B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 393 through 405 Processing helix chain 'C' and resid 22 through 49 removed outlier: 4.277A pdb=" N ASP C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 120 removed outlier: 3.680A pdb=" N TYR C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 144 Proline residue: C 128 - end of helix Processing helix chain 'C' and resid 152 through 166 Processing helix chain 'C' and resid 168 through 175 removed outlier: 4.011A pdb=" N THR C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 250 Processing helix chain 'C' and resid 256 through 284 removed outlier: 3.976A pdb=" N MET C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 263 " --> pdb=" O TYR C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 312 through 341 removed outlier: 3.908A pdb=" N PHE C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 359 removed outlier: 3.805A pdb=" N ARG C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 378 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 393 through 405 Processing helix chain 'D' and resid 22 through 47 removed outlier: 3.725A pdb=" N VAL D 26 " --> pdb=" O PRO D 22 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.814A pdb=" N TYR D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG D 118 " --> pdb=" O MET D 114 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.701A pdb=" N LYS D 125 " --> pdb=" O HIS D 121 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 126 " --> pdb=" O TRP D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 126' Processing helix chain 'D' and resid 126 through 143 removed outlier: 3.701A pdb=" N LEU D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN D 143 " --> pdb=" O MET D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 167 removed outlier: 3.987A pdb=" N LYS D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 3.917A pdb=" N THR D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 252 Processing helix chain 'D' and resid 259 through 283 removed outlier: 3.755A pdb=" N THR D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 283 " --> pdb=" O TYR D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 341 removed outlier: 3.668A pdb=" N PHE D 316 " --> pdb=" O MET D 312 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS D 318 " --> pdb=" O HIS D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 359 Processing helix chain 'D' and resid 367 through 378 removed outlier: 3.883A pdb=" N ALA D 371 " --> pdb=" O LYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.057A pdb=" N VAL D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 405 removed outlier: 3.546A pdb=" N GLU D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 22 through 49 removed outlier: 3.639A pdb=" N VAL E 47 " --> pdb=" O CYS E 43 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 120 removed outlier: 3.685A pdb=" N TYR E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 120 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 127 through 142 removed outlier: 3.623A pdb=" N VAL E 131 " --> pdb=" O PHE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 167 removed outlier: 3.902A pdb=" N PHE E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 176 removed outlier: 3.902A pdb=" N THR E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 253 removed outlier: 3.658A pdb=" N GLU E 253 " --> pdb=" O ARG E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 283 removed outlier: 3.514A pdb=" N LEU E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 287 removed outlier: 4.116A pdb=" N VAL E 287 " --> pdb=" O VAL E 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 287' Processing helix chain 'E' and resid 315 through 344 removed outlier: 3.747A pdb=" N ARG E 344 " --> pdb=" O TRP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 359 removed outlier: 3.628A pdb=" N ARG E 355 " --> pdb=" O PHE E 351 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 381 removed outlier: 3.579A pdb=" N GLN E 379 " --> pdb=" O HIS E 375 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 391 removed outlier: 3.999A pdb=" N PHE E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 405 removed outlier: 3.535A pdb=" N LEU E 405 " --> pdb=" O LYS E 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 49 removed outlier: 3.770A pdb=" N THR F 28 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 120 removed outlier: 3.813A pdb=" N TYR F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 127 through 143 removed outlier: 3.609A pdb=" N VAL F 131 " --> pdb=" O PHE F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 removed outlier: 4.289A pdb=" N LYS F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 167 removed outlier: 4.218A pdb=" N ASP F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 Processing helix chain 'F' and resid 232 through 253 Processing helix chain 'F' and resid 256 through 283 removed outlier: 4.478A pdb=" N TYR F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 342 removed outlier: 3.511A pdb=" N PHE F 316 " --> pdb=" O MET F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 367 through 378 Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.870A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 405 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 22 through 48 removed outlier: 3.635A pdb=" N VAL G 26 " --> pdb=" O PRO G 22 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL G 47 " --> pdb=" O CYS G 43 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET G 48 " --> pdb=" O THR G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 120 removed outlier: 3.755A pdb=" N TYR G 108 " --> pdb=" O ASP G 104 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU G 120 " --> pdb=" O TYR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.751A pdb=" N LYS G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 142 removed outlier: 3.701A pdb=" N LEU G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 148 removed outlier: 4.003A pdb=" N PHE G 148 " --> pdb=" O TRP G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 165 removed outlier: 4.081A pdb=" N ILE G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.637A pdb=" N THR G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 253 Processing helix chain 'G' and resid 259 through 283 removed outlier: 3.697A pdb=" N VAL G 263 " --> pdb=" O TYR G 259 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER G 281 " --> pdb=" O ILE G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 287 removed outlier: 3.727A pdb=" N VAL G 287 " --> pdb=" O VAL G 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 284 through 287' Processing helix chain 'G' and resid 312 through 342 removed outlier: 3.846A pdb=" N PHE G 316 " --> pdb=" O MET G 312 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LYS G 318 " --> pdb=" O HIS G 314 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G 319 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE G 321 " --> pdb=" O SER G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 359 Processing helix chain 'G' and resid 368 through 378 Processing helix chain 'G' and resid 379 through 381 No H-bonds generated for 'chain 'G' and resid 379 through 381' Processing helix chain 'G' and resid 382 through 390 removed outlier: 3.810A pdb=" N LYS G 386 " --> pdb=" O PRO G 382 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL G 390 " --> pdb=" O LYS G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 405 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 56 1057 hydrogen bonds defined for protein. 3141 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: 4.51 Time building geometry restraints manager: 6.91 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: 5193 1.34 - 1.46: 3708 1.46 - 1.58: 8844 1.58 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 17969 Sorted by residual: bond pdb=" N PRO A 22 " pdb=" CD PRO A 22 " ideal model delta sigma weight residual 1.473 1.506 -0.033 1.40e-02 5.10e+03 5.71e+00 bond pdb=" N ASN E 368 " pdb=" CA ASN E 368 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" C ARG D 249 " pdb=" N LEU D 250 " ideal model delta sigma weight residual 1.332 1.317 0.016 1.40e-02 5.10e+03 1.27e+00 bond pdb=" N ASN C 368 " pdb=" CA ASN C 368 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.23e+00 bond pdb=" CB GLU D 253 " pdb=" CG GLU D 253 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 ... (remaining 17964 not shown) Histogram of bond angle deviations from ideal: 98.05 - 105.25: 212 105.25 - 112.44: 8865 112.44 - 119.64: 6254 119.64 - 126.83: 8693 126.83 - 134.02: 234 Bond angle restraints: 24258 Sorted by residual: angle pdb=" C LYS B 51 " pdb=" CA LYS B 51 " pdb=" CB LYS B 51 " ideal model delta sigma weight residual 116.34 110.92 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" C ARG D 249 " pdb=" N LEU D 250 " pdb=" CA LEU D 250 " ideal model delta sigma weight residual 121.54 128.75 -7.21 1.91e+00 2.74e-01 1.42e+01 angle pdb=" N ILE E 257 " pdb=" CA ILE E 257 " pdb=" C ILE E 257 " ideal model delta sigma weight residual 113.53 110.57 2.96 9.80e-01 1.04e+00 9.15e+00 angle pdb=" C ALA B 278 " pdb=" N TYR B 279 " pdb=" CA TYR B 279 " ideal model delta sigma weight residual 121.58 115.70 5.88 1.95e+00 2.63e-01 9.08e+00 angle pdb=" C ALA A 278 " pdb=" N TYR A 279 " pdb=" CA TYR A 279 " ideal model delta sigma weight residual 122.38 117.11 5.27 1.81e+00 3.05e-01 8.48e+00 ... (remaining 24253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9412 17.98 - 35.96: 946 35.96 - 53.93: 178 53.93 - 71.91: 19 71.91 - 89.89: 27 Dihedral angle restraints: 10582 sinusoidal: 4307 harmonic: 6275 Sorted by residual: dihedral pdb=" CA ARG D 249 " pdb=" C ARG D 249 " pdb=" N LEU D 250 " pdb=" CA LEU D 250 " ideal model delta harmonic sigma weight residual 180.00 154.26 25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA LEU C 338 " pdb=" C LEU C 338 " pdb=" N TYR C 339 " pdb=" CA TYR C 339 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA PHE E 148 " pdb=" C PHE E 148 " pdb=" N PRO E 149 " pdb=" CA PRO E 149 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 10579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1679 0.030 - 0.060: 688 0.060 - 0.090: 197 0.090 - 0.119: 65 0.119 - 0.149: 18 Chirality restraints: 2647 Sorted by residual: chirality pdb=" CA ILE B 53 " pdb=" N ILE B 53 " pdb=" C ILE B 53 " pdb=" CB ILE B 53 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA VAL B 26 " pdb=" N VAL B 26 " pdb=" C VAL B 26 " pdb=" CB VAL B 26 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE B 363 " pdb=" N ILE B 363 " pdb=" C ILE B 363 " pdb=" CB ILE B 363 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 2644 not shown) Planarity restraints: 2955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 21 " 0.074 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO A 22 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 145 " -0.017 2.00e-02 2.50e+03 1.32e-02 4.33e+00 pdb=" CG TRP D 145 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP D 145 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP D 145 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 145 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 145 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 145 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 327 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C VAL A 327 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 327 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 328 " 0.011 2.00e-02 2.50e+03 ... (remaining 2952 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 501 2.71 - 3.26: 17667 3.26 - 3.81: 27495 3.81 - 4.35: 32102 4.35 - 4.90: 56504 Nonbonded interactions: 134269 Sorted by model distance: nonbonded pdb=" NE2 HIS A 134 " pdb=" OH TYR A 279 " model vdw 2.166 3.120 nonbonded pdb=" NE2 HIS G 134 " pdb=" OH TYR G 279 " model vdw 2.227 3.120 nonbonded pdb=" OH TYR D 123 " pdb=" OD1 ASN D 280 " model vdw 2.242 3.040 nonbonded pdb=" O PHE G 351 " pdb=" NE ARG G 355 " model vdw 2.248 3.120 nonbonded pdb=" NE2 HIS E 134 " pdb=" OH TYR E 279 " model vdw 2.254 3.120 ... (remaining 134264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'B' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'C' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'D' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'E' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'F' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'G' and (resid 16 through 175 or resid 177 or resid 235 through 405)) } 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 44.260 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.003 0.033 17969 Z= 0.201 Angle : 0.552 7.205 24258 Z= 0.313 Chirality : 0.037 0.149 2647 Planarity : 0.004 0.112 2955 Dihedral : 15.085 89.891 6478 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 2059 helix: 1.69 (0.15), residues: 1346 sheet: 0.18 (0.44), residues: 136 loop : -2.60 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 145 HIS 0.007 0.001 HIS C 310 PHE 0.031 0.002 PHE F 242 TYR 0.020 0.001 TYR C 279 ARG 0.004 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.989 Fit side-chains REVERT: A 347 ARG cc_start: 0.7326 (ptt180) cc_final: 0.6929 (mtm180) REVERT: A 373 MET cc_start: 0.7583 (mpp) cc_final: 0.7358 (mpp) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.3042 time to fit residues: 141.6470 Evaluate side-chains 261 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 251 HIS E 251 HIS E 288 GLN F 113 GLN F 121 HIS F 265 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN G 305 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17969 Z= 0.273 Angle : 0.565 7.202 24258 Z= 0.305 Chirality : 0.041 0.149 2647 Planarity : 0.004 0.059 2955 Dihedral : 4.302 29.601 2283 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.70 % Allowed : 10.67 % Favored : 87.63 % 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: 0.97 (0.20), residues: 2059 helix: 1.84 (0.15), residues: 1381 sheet: 0.12 (0.45), residues: 136 loop : -2.48 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 145 HIS 0.006 0.001 HIS C 310 PHE 0.024 0.002 PHE E 273 TYR 0.020 0.002 TYR C 279 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 282 time to evaluate : 2.004 Fit side-chains revert: symmetry clash REVERT: A 244 LYS cc_start: 0.8059 (ptpt) cc_final: 0.7842 (ptmt) REVERT: A 373 MET cc_start: 0.7934 (mpp) cc_final: 0.7274 (mpp) REVERT: B 21 LYS cc_start: 0.7683 (tptp) cc_final: 0.7464 (mmtm) REVERT: D 373 MET cc_start: 0.6625 (tpp) cc_final: 0.6208 (tpt) REVERT: F 147 LYS cc_start: 0.8771 (ttmt) cc_final: 0.7904 (tppt) outliers start: 33 outliers final: 28 residues processed: 302 average time/residue: 0.3200 time to fit residues: 141.0177 Evaluate side-chains 295 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 267 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain G residue 241 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 0.0570 chunk 58 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 128 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS E 288 GLN F 106 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17969 Z= 0.151 Angle : 0.474 6.706 24258 Z= 0.255 Chirality : 0.038 0.150 2647 Planarity : 0.003 0.044 2955 Dihedral : 4.074 24.668 2283 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.06 % Allowed : 12.89 % Favored : 85.05 % 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: 1.29 (0.20), residues: 2059 helix: 2.06 (0.15), residues: 1386 sheet: 0.27 (0.46), residues: 136 loop : -2.37 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 145 HIS 0.003 0.001 HIS C 310 PHE 0.019 0.001 PHE G 388 TYR 0.019 0.001 TYR F 349 ARG 0.004 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 301 time to evaluate : 2.061 Fit side-chains revert: symmetry clash REVERT: A 244 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7880 (ptmt) REVERT: A 347 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.5695 (ttm170) REVERT: A 373 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7772 (mpp) REVERT: D 249 ARG cc_start: 0.8479 (ptm160) cc_final: 0.8232 (ptm160) REVERT: F 143 ASN cc_start: 0.7127 (m-40) cc_final: 0.6685 (t0) REVERT: F 147 LYS cc_start: 0.8722 (ttmt) cc_final: 0.7964 (tppt) outliers start: 40 outliers final: 30 residues processed: 318 average time/residue: 0.3147 time to fit residues: 145.3094 Evaluate side-chains 316 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 284 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 145 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 392 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 98 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS D 107 GLN E 49 GLN E 251 HIS E 288 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17969 Z= 0.177 Angle : 0.483 6.158 24258 Z= 0.259 Chirality : 0.038 0.215 2647 Planarity : 0.003 0.040 2955 Dihedral : 3.986 25.093 2283 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.99 % Allowed : 14.12 % Favored : 82.89 % 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: 1.28 (0.20), residues: 2059 helix: 2.04 (0.15), residues: 1397 sheet: 0.25 (0.46), residues: 136 loop : -2.41 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 145 HIS 0.004 0.001 HIS C 310 PHE 0.018 0.001 PHE D 248 TYR 0.018 0.001 TYR B 380 ARG 0.003 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 291 time to evaluate : 1.952 Fit side-chains revert: symmetry clash REVERT: A 347 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.5565 (ttm170) REVERT: A 373 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7734 (mpp) REVERT: B 376 MET cc_start: 0.8113 (tpp) cc_final: 0.7880 (mmm) REVERT: F 143 ASN cc_start: 0.7068 (m-40) cc_final: 0.6620 (t0) REVERT: F 147 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8007 (tppt) REVERT: G 45 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7689 (tt) REVERT: G 105 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8600 (tt) outliers start: 58 outliers final: 41 residues processed: 328 average time/residue: 0.3125 time to fit residues: 150.0118 Evaluate side-chains 322 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 277 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 145 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 392 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 0.4980 chunk 114 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 138 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 106 GLN C 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS E 288 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17969 Z= 0.191 Angle : 0.496 8.308 24258 Z= 0.264 Chirality : 0.039 0.141 2647 Planarity : 0.003 0.040 2955 Dihedral : 3.980 25.204 2283 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.09 % Allowed : 15.62 % Favored : 81.29 % 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: 1.25 (0.20), residues: 2059 helix: 2.03 (0.15), residues: 1396 sheet: 0.21 (0.46), residues: 136 loop : -2.44 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 170 HIS 0.004 0.001 HIS C 310 PHE 0.023 0.001 PHE D 242 TYR 0.020 0.001 TYR B 380 ARG 0.003 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 276 time to evaluate : 1.803 Fit side-chains REVERT: A 347 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.5412 (ttm170) REVERT: A 373 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7721 (mpp) REVERT: B 21 LYS cc_start: 0.7865 (tptp) cc_final: 0.7601 (mmtm) REVERT: F 143 ASN cc_start: 0.7163 (m-40) cc_final: 0.6704 (t0) REVERT: F 147 LYS cc_start: 0.8715 (ttmt) cc_final: 0.7995 (tppt) REVERT: G 45 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7734 (tt) REVERT: G 105 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8537 (tt) outliers start: 60 outliers final: 50 residues processed: 313 average time/residue: 0.3030 time to fit residues: 139.5163 Evaluate side-chains 324 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 270 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 145 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 265 GLN Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 392 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 69.7238 > 50: distance: 12 - 17: 25.440 distance: 17 - 18: 33.895 distance: 18 - 19: 11.265 distance: 18 - 21: 11.661 distance: 22 - 162: 35.221 distance: 23 - 156: 35.588 distance: 24 - 25: 15.023 distance: 25 - 26: 42.834 distance: 25 - 31: 25.958 distance: 26 - 153: 35.589 distance: 28 - 30: 41.021 distance: 31 - 32: 52.003 distance: 31 - 37: 40.838 distance: 32 - 35: 44.860 distance: 33 - 38: 39.336 distance: 35 - 36: 20.941 distance: 36 - 37: 15.092 distance: 40 - 41: 40.289 distance: 42 - 43: 56.666 distance: 43 - 44: 39.122 distance: 44 - 45: 40.981 distance: 45 - 46: 56.663 distance: 47 - 48: 40.042 distance: 48 - 49: 30.743 distance: 48 - 51: 45.659 distance: 49 - 50: 11.394 distance: 49 - 58: 49.353 distance: 51 - 52: 20.094 distance: 52 - 53: 12.499 distance: 53 - 54: 24.111 distance: 54 - 55: 27.744 distance: 55 - 56: 43.782 distance: 55 - 57: 57.810 distance: 58 - 59: 16.697 distance: 59 - 60: 49.487 distance: 59 - 62: 26.432 distance: 60 - 61: 35.597 distance: 62 - 63: 19.434 distance: 62 - 64: 20.591 distance: 65 - 66: 19.284 distance: 66 - 67: 20.636 distance: 66 - 69: 13.256 distance: 67 - 68: 26.282 distance: 67 - 74: 52.420 distance: 69 - 70: 13.988 distance: 70 - 71: 21.921 distance: 71 - 72: 25.017 distance: 71 - 73: 25.032 distance: 74 - 75: 16.299 distance: 75 - 76: 19.919 distance: 75 - 78: 26.887 distance: 76 - 82: 16.057 distance: 78 - 79: 44.314 distance: 79 - 80: 40.553 distance: 80 - 81: 13.804 distance: 82 - 83: 37.258 distance: 83 - 84: 42.409 distance: 83 - 86: 27.382 distance: 84 - 91: 56.263 distance: 86 - 87: 56.835 distance: 87 - 88: 54.722 distance: 88 - 89: 15.780 distance: 89 - 90: 11.574 distance: 91 - 92: 39.920 distance: 92 - 93: 69.282 distance: 93 - 95: 35.486