Starting phenix.real_space_refine on Sat Dec 9 23:06:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vff_31951/12_2023/7vff_31951.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vff_31951/12_2023/7vff_31951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vff_31951/12_2023/7vff_31951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vff_31951/12_2023/7vff_31951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vff_31951/12_2023/7vff_31951.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vff_31951/12_2023/7vff_31951.pdb" } resolution = 4.1 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= 1.000 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 36 5.16 5 C 8043 2.51 5 N 2043 2.21 5 O 2457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C ASP 333": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12579 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4193 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Chain: "B" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4193 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Chain: "C" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4193 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ARG A 83 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG A 83 " occ=0.50 residue: pdb=" N ARG B 83 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG B 83 " occ=0.50 residue: pdb=" N ARG C 83 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG C 83 " occ=0.50 Time building chain proxies: 6.74, per 1000 atoms: 0.54 Number of scatterers: 12579 At special positions: 0 Unit cell: (99.68, 104.16, 106.4, 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 36 16.00 O 2457 8.00 N 2043 7.00 C 8043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 2.5 seconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 33 sheets defined 20.3% alpha, 43.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.696A pdb=" N VAL A 164 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 279 through 295 removed outlier: 4.169A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.865A pdb=" N TRP A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 401' Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.696A pdb=" N VAL B 164 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 279 through 295 removed outlier: 4.170A pdb=" N ASP B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.865A pdb=" N TRP B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 401' Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.696A pdb=" N VAL C 164 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 279 through 295 removed outlier: 4.169A pdb=" N ASP C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 395 Processing helix chain 'C' and resid 396 through 401 removed outlier: 3.866A pdb=" N TRP C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 401' Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 516 through 521 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.951A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 69 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.951A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 removed outlier: 7.157A pdb=" N ASN A 96 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU A 111 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 98 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU A 109 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A 100 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.941A pdb=" N VAL A 78 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 141 removed outlier: 5.729A pdb=" N ARG A 83 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 236 removed outlier: 4.473A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 252 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.857A pdb=" N ARG A 475 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 247 removed outlier: 6.318A pdb=" N LYS A 502 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE A 447 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER A 504 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL A 445 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A 506 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU A 443 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 508 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE A 447 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 296 through 299 Processing sheet with id=AB1, first strand: chain 'A' and resid 320 through 323 removed outlier: 6.760A pdb=" N ASP A 327 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE A 368 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR A 329 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY A 370 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS A 331 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR A 372 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP A 333 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE A 365 " --> pdb=" O HIS A 386 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N HIS A 386 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA A 367 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE A 384 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR A 369 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 378 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AB3, first strand: chain 'B' and resid 32 through 40 removed outlier: 3.951A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU B 69 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 32 through 40 removed outlier: 3.951A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 44 removed outlier: 7.157A pdb=" N ASN B 96 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU B 111 " --> pdb=" O ASN B 96 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 98 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU B 109 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 100 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.942A pdb=" N VAL B 78 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 139 through 141 removed outlier: 5.729A pdb=" N ARG B 83 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 227 through 236 removed outlier: 4.473A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 252 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.857A pdb=" N ARG B 475 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 243 through 247 removed outlier: 6.317A pdb=" N LYS B 502 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE B 447 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER B 504 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL B 445 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG B 506 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU B 443 " --> pdb=" O ARG B 506 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 508 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 447 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 296 through 299 Processing sheet with id=AC3, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.760A pdb=" N ASP B 327 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE B 368 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR B 329 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY B 370 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS B 331 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR B 372 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP B 333 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE B 365 " --> pdb=" O HIS B 386 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N HIS B 386 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 367 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE B 384 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR B 369 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 378 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AC5, first strand: chain 'C' and resid 32 through 40 removed outlier: 3.952A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 69 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 32 through 40 removed outlier: 3.952A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 42 through 44 removed outlier: 7.158A pdb=" N ASN C 96 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU C 111 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 98 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU C 109 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE C 100 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.941A pdb=" N VAL C 78 " --> pdb=" O ILE C 148 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 139 through 141 removed outlier: 5.729A pdb=" N ARG C 83 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 227 through 236 removed outlier: 4.473A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 252 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.857A pdb=" N ARG C 475 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 243 through 247 removed outlier: 6.318A pdb=" N LYS C 502 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE C 447 " --> pdb=" O LYS C 502 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER C 504 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL C 445 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG C 506 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU C 443 " --> pdb=" O ARG C 506 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL C 508 " --> pdb=" O SER C 441 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE C 447 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 296 through 299 Processing sheet with id=AD5, first strand: chain 'C' and resid 320 through 323 removed outlier: 6.760A pdb=" N ASP C 327 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE C 368 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR C 329 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY C 370 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS C 331 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR C 372 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP C 333 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS C 383 " --> pdb=" O THR C 369 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR C 371 " --> pdb=" O PHE C 381 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE C 381 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER C 373 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N THR C 379 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 349 through 350 515 hydrogen bonds defined for protein. 1365 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: 4.39 Time building geometry restraints manager: 5.03 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: 3989 1.34 - 1.45: 1878 1.45 - 1.57: 6928 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 12855 Sorted by residual: bond pdb=" N TYR C 453 " pdb=" CA TYR C 453 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.18e-02 7.18e+03 5.51e+00 bond pdb=" N TYR A 453 " pdb=" CA TYR A 453 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.18e-02 7.18e+03 5.46e+00 bond pdb=" N TYR B 453 " pdb=" CA TYR B 453 " ideal model delta sigma weight residual 1.455 1.483 -0.027 1.18e-02 7.18e+03 5.39e+00 bond pdb=" N TYR C 359 " pdb=" CA TYR C 359 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.04e+00 bond pdb=" N TYR A 359 " pdb=" CA TYR A 359 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.00e+00 ... (remaining 12850 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.00: 268 106.00 - 113.00: 7078 113.00 - 120.01: 4358 120.01 - 127.01: 5681 127.01 - 134.01: 105 Bond angle restraints: 17490 Sorted by residual: angle pdb=" CA ASP A 333 " pdb=" C ASP A 333 " pdb=" O ASP A 333 " ideal model delta sigma weight residual 121.72 117.99 3.73 1.18e+00 7.18e-01 9.98e+00 angle pdb=" CA ASP B 333 " pdb=" C ASP B 333 " pdb=" O ASP B 333 " ideal model delta sigma weight residual 121.72 118.02 3.70 1.18e+00 7.18e-01 9.84e+00 angle pdb=" CA ASP C 333 " pdb=" C ASP C 333 " pdb=" O ASP C 333 " ideal model delta sigma weight residual 121.72 118.03 3.69 1.18e+00 7.18e-01 9.76e+00 angle pdb=" CA TYR C 359 " pdb=" C TYR C 359 " pdb=" O TYR C 359 " ideal model delta sigma weight residual 120.58 117.66 2.92 1.07e+00 8.73e-01 7.46e+00 angle pdb=" CA TYR B 359 " pdb=" C TYR B 359 " pdb=" O TYR B 359 " ideal model delta sigma weight residual 120.58 117.66 2.92 1.07e+00 8.73e-01 7.45e+00 ... (remaining 17485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 6994 17.48 - 34.96: 600 34.96 - 52.45: 86 52.45 - 69.93: 15 69.93 - 87.41: 24 Dihedral angle restraints: 7719 sinusoidal: 3036 harmonic: 4683 Sorted by residual: dihedral pdb=" CA PRO A 483 " pdb=" C PRO A 483 " pdb=" N LYS A 484 " pdb=" CA LYS A 484 " ideal model delta harmonic sigma weight residual -180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PRO B 483 " pdb=" C PRO B 483 " pdb=" N LYS B 484 " pdb=" CA LYS B 484 " ideal model delta harmonic sigma weight residual 180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PRO C 483 " pdb=" C PRO C 483 " pdb=" N LYS C 484 " pdb=" CA LYS C 484 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 7716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1262 0.044 - 0.088: 504 0.088 - 0.132: 232 0.132 - 0.176: 12 0.176 - 0.220: 6 Chirality restraints: 2016 Sorted by residual: chirality pdb=" CA TYR C 359 " pdb=" N TYR C 359 " pdb=" C TYR C 359 " pdb=" CB TYR C 359 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA TYR A 359 " pdb=" N TYR A 359 " pdb=" C TYR A 359 " pdb=" CB TYR A 359 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA TYR B 359 " pdb=" N TYR B 359 " pdb=" C TYR B 359 " pdb=" CB TYR B 359 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2013 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 209 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO B 210 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 209 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 210 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 209 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO C 210 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 210 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 210 " 0.029 5.00e-02 4.00e+02 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4280 2.85 - 3.36: 10495 3.36 - 3.87: 20247 3.87 - 4.39: 22484 4.39 - 4.90: 39944 Nonbonded interactions: 97450 Sorted by model distance: nonbonded pdb=" OG SER C 322 " pdb=" OD1 ASP C 327 " model vdw 2.334 2.440 nonbonded pdb=" OG SER B 322 " pdb=" OD1 ASP B 327 " model vdw 2.334 2.440 nonbonded pdb=" OG SER A 322 " pdb=" OD1 ASP A 327 " model vdw 2.335 2.440 nonbonded pdb=" O PHE B 22 " pdb=" NZ LYS C 172 " model vdw 2.355 2.520 nonbonded pdb=" NE2 HIS A 128 " pdb=" OE1 GLU B 465 " model vdw 2.390 2.520 ... (remaining 97445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.710 Set stop_for_unknowns flag: 0.010 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: 4.010 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 34.830 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 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 : 0.007 0.064 12855 Z= 0.467 Angle : 0.723 8.446 17490 Z= 0.411 Chirality : 0.054 0.220 2016 Planarity : 0.005 0.052 2235 Dihedral : 13.866 87.411 4707 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.41 % Allowed : 4.95 % Favored : 94.64 % 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: -0.82 (0.19), residues: 1569 helix: -1.03 (0.29), residues: 237 sheet: 0.06 (0.22), residues: 462 loop : -0.67 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 108 HIS 0.004 0.001 HIS A 97 PHE 0.028 0.003 PHE B 479 TYR 0.023 0.002 TYR C 157 ARG 0.021 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 425 time to evaluate : 1.579 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 428 average time/residue: 0.2573 time to fit residues: 154.9373 Evaluate side-chains 212 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 1.585 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1146 time to fit residues: 2.7667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 141 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 97 HIS ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN B 97 HIS C 97 HIS C 480 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12855 Z= 0.238 Angle : 0.545 9.973 17490 Z= 0.295 Chirality : 0.049 0.151 2016 Planarity : 0.004 0.030 2235 Dihedral : 4.679 19.001 1725 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.53 % 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: -0.12 (0.20), residues: 1569 helix: -0.14 (0.34), residues: 234 sheet: 0.36 (0.23), residues: 474 loop : -0.22 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 108 HIS 0.003 0.001 HIS C 344 PHE 0.015 0.001 PHE A 228 TYR 0.018 0.001 TYR C 208 ARG 0.003 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 265 average time/residue: 0.2207 time to fit residues: 87.6431 Evaluate side-chains 192 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.514 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 69.6308 > 50: distance: 21 - 26: 30.585 distance: 26 - 27: 6.422 distance: 27 - 28: 21.849 distance: 27 - 30: 64.498 distance: 28 - 29: 55.380 distance: 28 - 34: 30.220 distance: 30 - 31: 42.803 distance: 31 - 32: 7.146 distance: 31 - 33: 9.657 distance: 34 - 35: 9.156 distance: 35 - 36: 57.958 distance: 35 - 38: 16.108 distance: 36 - 37: 38.173 distance: 36 - 43: 44.380 distance: 38 - 39: 52.569 distance: 39 - 40: 12.625 distance: 40 - 41: 31.878 distance: 40 - 42: 28.386 distance: 43 - 44: 37.390 distance: 43 - 49: 20.789 distance: 44 - 45: 14.876 distance: 44 - 47: 56.080 distance: 45 - 46: 34.364 distance: 45 - 50: 38.753 distance: 47 - 48: 16.511 distance: 48 - 49: 37.481 distance: 50 - 51: 7.154 distance: 51 - 52: 15.761 distance: 51 - 54: 23.896 distance: 52 - 53: 7.929 distance: 52 - 57: 29.857 distance: 54 - 55: 16.626 distance: 54 - 56: 5.535 distance: 57 - 58: 23.507 distance: 57 - 147: 16.238 distance: 58 - 59: 20.382 distance: 58 - 61: 13.263 distance: 59 - 60: 25.494 distance: 59 - 62: 31.933 distance: 60 - 144: 21.560 distance: 62 - 63: 30.868 distance: 63 - 66: 49.842 distance: 64 - 65: 28.671 distance: 64 - 69: 54.812 distance: 66 - 67: 33.002 distance: 66 - 68: 15.207 distance: 69 - 70: 21.377 distance: 69 - 135: 27.733 distance: 70 - 71: 61.447 distance: 70 - 73: 36.977 distance: 71 - 72: 44.237 distance: 71 - 76: 45.537 distance: 72 - 132: 34.994 distance: 73 - 74: 24.892 distance: 73 - 75: 29.399 distance: 76 - 77: 47.691 distance: 77 - 78: 28.899 distance: 77 - 80: 21.447 distance: 78 - 79: 23.491 distance: 78 - 83: 43.914 distance: 80 - 81: 12.430 distance: 80 - 82: 13.238 distance: 83 - 84: 25.345 distance: 84 - 85: 27.485 distance: 84 - 87: 39.731 distance: 85 - 86: 29.446 distance: 85 - 92: 48.188 distance: 87 - 88: 13.936 distance: 88 - 89: 6.954 distance: 89 - 90: 22.380 distance: 89 - 91: 26.646 distance: 92 - 93: 19.916 distance: 93 - 94: 22.804 distance: 93 - 96: 24.780 distance: 94 - 95: 16.553 distance: 94 - 99: 20.939 distance: 96 - 97: 18.512 distance: 96 - 98: 25.776