Starting phenix.real_space_refine on Wed Dec 13 03:34:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/12_2023/6umm_20820.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/12_2023/6umm_20820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/12_2023/6umm_20820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/12_2023/6umm_20820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/12_2023/6umm_20820.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/12_2023/6umm_20820.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 60 5.16 5 C 15131 2.51 5 N 4240 2.21 5 O 4227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 27": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A ASP 190": "OD1" <-> "OD2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "B ARG 11": "NH1" <-> "NH2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ASP 378": "OD1" <-> "OD2" Residue "B TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 445": "NH1" <-> "NH2" Residue "B PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 455": "OD1" <-> "OD2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "C ASP 19": "OD1" <-> "OD2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C ARG 406": "NH1" <-> "NH2" Residue "C ASP 437": "OD1" <-> "OD2" Residue "C TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "D PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E GLU 179": "OE1" <-> "OE2" Residue "E ASP 181": "OD1" <-> "OD2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E ARG 225": "NH1" <-> "NH2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "E ASP 268": "OD1" <-> "OD2" Residue "E ASP 274": "OD1" <-> "OD2" Residue "E ARG 280": "NH1" <-> "NH2" Residue "E ARG 290": "NH1" <-> "NH2" Residue "E ARG 292": "NH1" <-> "NH2" Residue "E ASP 299": "OD1" <-> "OD2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E GLU 350": "OE1" <-> "OE2" Residue "E TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 354": "OD1" <-> "OD2" Residue "E ARG 361": "NH1" <-> "NH2" Residue "E ARG 366": "NH1" <-> "NH2" Residue "E ARG 395": "NH1" <-> "NH2" Residue "E ARG 399": "NH1" <-> "NH2" Residue "F ARG 27": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "F ARG 118": "NH1" <-> "NH2" Residue "F ARG 119": "NH1" <-> "NH2" Residue "F ASP 127": "OD1" <-> "OD2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 154": "NH1" <-> "NH2" Residue "F GLU 161": "OE1" <-> "OE2" Residue "F ASP 173": "OD1" <-> "OD2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F ASP 190": "OD1" <-> "OD2" Residue "F ASP 206": "OD1" <-> "OD2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F GLU 219": "OE1" <-> "OE2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 246": "NH1" <-> "NH2" Residue "F ARG 260": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ASP 19": "OD1" <-> "OD2" Residue "G ASP 20": "OD1" <-> "OD2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G ASP 114": "OD1" <-> "OD2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G ARG 125": "NH1" <-> "NH2" Residue "G ASP 160": "OD1" <-> "OD2" Residue "G ASP 211": "OD1" <-> "OD2" Residue "G ARG 239": "NH1" <-> "NH2" Residue "G ARG 295": "NH1" <-> "NH2" Residue "G ASP 405": "OD1" <-> "OD2" Residue "G ARG 406": "NH1" <-> "NH2" Residue "G TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 444": "NH1" <-> "NH2" Residue "G ARG 445": "NH1" <-> "NH2" Residue "G ASP 455": "OD1" <-> "OD2" Residue "G ARG 475": "NH1" <-> "NH2" Residue "H ASP 19": "OD1" <-> "OD2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 84": "OD1" <-> "OD2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H ARG 155": "NH1" <-> "NH2" Residue "H ASP 211": "OD1" <-> "OD2" Residue "H ASP 306": "OD1" <-> "OD2" Residue "H ARG 312": "NH1" <-> "NH2" Residue "H ARG 406": "NH1" <-> "NH2" Residue "H ASP 437": "OD1" <-> "OD2" Residue "H TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 474": "OD1" <-> "OD2" Residue "I ASP 62": "OD1" <-> "OD2" Residue "I ARG 65": "NH1" <-> "NH2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "J ARG 3": "NH1" <-> "NH2" Residue "J GLU 25": "OE1" <-> "OE2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J ASP 103": "OD1" <-> "OD2" Residue "J ARG 112": "NH1" <-> "NH2" Residue "J ASP 113": "OD1" <-> "OD2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "J ASP 149": "OD1" <-> "OD2" Residue "J ARG 151": "NH1" <-> "NH2" Residue "J PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 168": "OD1" <-> "OD2" Residue "J ASP 181": "OD1" <-> "OD2" Residue "J ARG 191": "NH1" <-> "NH2" Residue "J ARG 198": "NH1" <-> "NH2" Residue "J GLU 220": "OE1" <-> "OE2" Residue "J ARG 225": "NH1" <-> "NH2" Residue "J ARG 280": "NH1" <-> "NH2" Residue "J ARG 290": "NH1" <-> "NH2" Residue "J ARG 292": "NH1" <-> "NH2" Residue "J ARG 300": "NH1" <-> "NH2" Residue "J ASP 322": "OD1" <-> "OD2" Residue "J GLU 345": "OE1" <-> "OE2" Residue "J ARG 349": "NH1" <-> "NH2" Residue "J TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 361": "NH1" <-> "NH2" Residue "J ASP 364": "OD1" <-> "OD2" Residue "J ARG 366": "NH1" <-> "NH2" Residue "J ARG 395": "NH1" <-> "NH2" Residue "J ARG 399": "NH1" <-> "NH2" Residue "J ASP 401": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 23658 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2169 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 268} Chain: "B" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3162 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 415} Chain breaks: 2 Chain: "C" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3238 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 422} Chain breaks: 1 Chain: "D" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 644 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "E" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2698 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 313} Chain breaks: 1 Chain: "F" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2169 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 268} Chain: "G" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3162 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 415} Chain breaks: 2 Chain: "H" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3238 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 422} Chain breaks: 1 Chain: "I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "J" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2698 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 313} Chain breaks: 1 Time building chain proxies: 12.66, per 1000 atoms: 0.54 Number of scatterers: 23658 At special positions: 0 Unit cell: (188.6, 141.86, 154.98, 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 60 16.00 O 4227 8.00 N 4240 7.00 C 15131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.00 Conformation dependent library (CDL) restraints added in 4.2 seconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5908 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 19 sheets defined 58.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 Processing helix chain 'A' and resid 23 through 41 Processing helix chain 'A' and resid 48 through 65 Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.671A pdb=" N VAL A 93 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.793A pdb=" N LEU A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 163 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 263 through 270 Processing helix chain 'B' and resid 34 through 47 removed outlier: 3.796A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 111 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 127 through 159 removed outlier: 3.803A pdb=" N HIS B 131 " --> pdb=" O TRP B 127 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 181 removed outlier: 3.675A pdb=" N LEU B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 213 through 234 removed outlier: 3.553A pdb=" N GLY B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 264 Processing helix chain 'B' and resid 267 through 285 removed outlier: 3.556A pdb=" N ILE B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 319 through 351 Processing helix chain 'B' and resid 356 through 374 removed outlier: 3.556A pdb=" N TRP B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 removed outlier: 4.396A pdb=" N SER B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 430 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 436 through 439 removed outlier: 3.540A pdb=" N TYR B 439 " --> pdb=" O PRO B 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 436 through 439' Processing helix chain 'B' and resid 440 through 455 Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.984A pdb=" N VAL B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'C' and resid 34 through 47 Proline residue: C 40 - end of helix Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 115 through 123 removed outlier: 3.926A pdb=" N ARG C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 158 Processing helix chain 'C' and resid 161 through 182 Processing helix chain 'C' and resid 185 through 196 removed outlier: 3.543A pdb=" N ALA C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 208 removed outlier: 3.889A pdb=" N LEU C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 removed outlier: 3.587A pdb=" N VAL C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 264 removed outlier: 3.753A pdb=" N VAL C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 285 Processing helix chain 'C' and resid 285 through 294 Processing helix chain 'C' and resid 313 through 351 removed outlier: 3.667A pdb=" N LEU C 317 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Proline residue: C 321 - end of helix Processing helix chain 'C' and resid 356 through 373 Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 379 through 404 removed outlier: 4.648A pdb=" N SER C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 430 Processing helix chain 'C' and resid 435 through 439 Processing helix chain 'C' and resid 440 through 466 removed outlier: 4.443A pdb=" N ILE C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) Proline residue: C 460 - end of helix Processing helix chain 'C' and resid 467 through 474 Processing helix chain 'D' and resid 34 through 54 Processing helix chain 'D' and resid 62 through 92 Processing helix chain 'E' and resid 95 through 130 Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.540A pdb=" N ILE E 139 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 197 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 220 through 237 Processing helix chain 'E' and resid 258 through 264 Processing helix chain 'E' and resid 285 through 298 Proline residue: E 295 - end of helix Processing helix chain 'E' and resid 386 through 399 removed outlier: 3.953A pdb=" N ARG E 399 " --> pdb=" O ARG E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 17 Processing helix chain 'F' and resid 23 through 41 Processing helix chain 'F' and resid 48 through 65 Processing helix chain 'F' and resid 89 through 96 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 143 through 163 Processing helix chain 'F' and resid 204 through 215 removed outlier: 3.638A pdb=" N VAL F 208 " --> pdb=" O ARG F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 271 Processing helix chain 'G' and resid 34 through 37 Processing helix chain 'G' and resid 38 through 47 Processing helix chain 'G' and resid 112 through 121 removed outlier: 3.585A pdb=" N GLU G 121 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 159 Processing helix chain 'G' and resid 161 through 181 removed outlier: 3.805A pdb=" N PHE G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 208 removed outlier: 3.664A pdb=" N ALA G 189 " --> pdb=" O SER G 185 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL G 198 " --> pdb=" O VAL G 194 " (cutoff:3.500A) Proline residue: G 199 - end of helix removed outlier: 3.993A pdb=" N VAL G 208 " --> pdb=" O PHE G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 235 removed outlier: 3.616A pdb=" N VAL G 217 " --> pdb=" O GLY G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 264 Processing helix chain 'G' and resid 267 through 285 removed outlier: 3.501A pdb=" N ILE G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 294 Processing helix chain 'G' and resid 319 through 349 Processing helix chain 'G' and resid 356 through 374 Processing helix chain 'G' and resid 379 through 404 removed outlier: 3.518A pdb=" N TRP G 385 " --> pdb=" O ALA G 381 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER G 390 " --> pdb=" O LEU G 386 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR G 391 " --> pdb=" O LEU G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 430 removed outlier: 3.552A pdb=" N ALA G 410 " --> pdb=" O ARG G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 435 removed outlier: 3.634A pdb=" N ALA G 434 " --> pdb=" O ASN G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 466 removed outlier: 5.280A pdb=" N ILE G 459 " --> pdb=" O ASP G 455 " (cutoff:3.500A) Proline residue: G 460 - end of helix Processing helix chain 'G' and resid 469 through 474 Processing helix chain 'H' and resid 34 through 47 removed outlier: 3.980A pdb=" N ILE H 38 " --> pdb=" O PRO H 34 " (cutoff:3.500A) Proline residue: H 40 - end of helix removed outlier: 3.518A pdb=" N GLN H 47 " --> pdb=" O GLN H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 115 through 123 Processing helix chain 'H' and resid 128 through 158 Processing helix chain 'H' and resid 160 through 181 removed outlier: 4.408A pdb=" N GLN H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 186 through 196 Processing helix chain 'H' and resid 196 through 206 Processing helix chain 'H' and resid 213 through 233 removed outlier: 4.021A pdb=" N VAL H 217 " --> pdb=" O GLY H 213 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 233 " --> pdb=" O LEU H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 264 removed outlier: 3.534A pdb=" N TRP H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 285 removed outlier: 3.527A pdb=" N ILE H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN H 285 " --> pdb=" O ILE H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 294 Processing helix chain 'H' and resid 313 through 351 removed outlier: 3.531A pdb=" N LEU H 317 " --> pdb=" O PRO H 313 " (cutoff:3.500A) Proline residue: H 321 - end of helix Processing helix chain 'H' and resid 356 through 373 Processing helix chain 'H' and resid 380 through 404 removed outlier: 3.846A pdb=" N ALA H 384 " --> pdb=" O ALA H 380 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER H 390 " --> pdb=" O LEU H 386 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR H 391 " --> pdb=" O LEU H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 430 Processing helix chain 'H' and resid 435 through 439 Processing helix chain 'H' and resid 440 through 466 removed outlier: 4.331A pdb=" N ILE H 459 " --> pdb=" O ASP H 455 " (cutoff:3.500A) Proline residue: H 460 - end of helix Processing helix chain 'H' and resid 468 through 475 Processing helix chain 'I' and resid 34 through 51 Processing helix chain 'I' and resid 62 through 92 Processing helix chain 'J' and resid 95 through 130 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'J' and resid 183 through 197 Processing helix chain 'J' and resid 210 through 212 No H-bonds generated for 'chain 'J' and resid 210 through 212' Processing helix chain 'J' and resid 220 through 237 Processing helix chain 'J' and resid 255 through 260 removed outlier: 4.226A pdb=" N TRP J 260 " --> pdb=" O GLY J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 263 No H-bonds generated for 'chain 'J' and resid 261 through 263' Processing helix chain 'J' and resid 285 through 294 Processing helix chain 'J' and resid 295 through 297 No H-bonds generated for 'chain 'J' and resid 295 through 297' Processing helix chain 'J' and resid 324 through 328 removed outlier: 3.623A pdb=" N ILE J 328 " --> pdb=" O PRO J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 398 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 169 removed outlier: 4.401A pdb=" N VAL A 79 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A 120 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.305A pdb=" N ASP A 105 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY A 228 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 219 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL A 237 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 199 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 181 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.647A pdb=" N LYS A 181 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 169 removed outlier: 4.401A pdb=" N VAL A 79 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP A 127 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS A 104 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP A 105 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY A 228 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 219 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL A 237 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 199 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 67 through 71 removed outlier: 8.836A pdb=" N LEU B 94 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 13 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU B 96 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU B 15 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N ALA B 98 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 14 Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AA8, first strand: chain 'E' and resid 22 through 24 removed outlier: 6.039A pdb=" N ILE E 22 " --> pdb=" O LYS E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 157 through 166 removed outlier: 6.793A pdb=" N VAL E 157 " --> pdb=" O ASP E 208 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP E 208 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG E 159 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY E 206 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY E 161 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N HIS E 163 " --> pdb=" O ASP E 202 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 202 " --> pdb=" O HIS E 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 246 through 249 removed outlier: 6.225A pdb=" N ALA E 247 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL E 316 " --> pdb=" O ILE E 340 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG E 342 " --> pdb=" O VAL E 316 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU E 318 " --> pdb=" O ARG E 342 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU E 360 " --> pdb=" O ARG E 214 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR E 216 " --> pdb=" O LEU E 360 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL E 362 " --> pdb=" O THR E 216 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE E 218 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE E 359 " --> pdb=" O TRP E 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 166 through 168 removed outlier: 3.868A pdb=" N SER F 120 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS F 106 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER F 229 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL F 237 " --> pdb=" O VAL F 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 98 through 99 Processing sheet with id=AB4, first strand: chain 'F' and resid 181 through 182 Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 71 removed outlier: 8.471A pdb=" N LEU G 94 " --> pdb=" O ARG G 11 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA G 13 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU G 96 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU G 15 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N ALA G 98 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG G 23 " --> pdb=" O ALA G 16 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 24 through 30 removed outlier: 3.918A pdb=" N LEU H 96 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 23 through 24 Processing sheet with id=AB8, first strand: chain 'J' and resid 157 through 163 removed outlier: 6.938A pdb=" N THR J 205 " --> pdb=" O ALA J 160 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG J 162 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ALA J 203 " --> pdb=" O ARG J 162 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 216 through 219 removed outlier: 5.824A pdb=" N THR J 216 " --> pdb=" O LEU J 360 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL J 362 " --> pdb=" O THR J 216 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE J 218 " --> pdb=" O VAL J 362 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE J 359 " --> pdb=" O TRP J 370 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 246 through 248 removed outlier: 6.429A pdb=" N ALA J 247 " --> pdb=" O VAL J 317 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU J 314 " --> pdb=" O THR J 338 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE J 340 " --> pdb=" O LEU J 314 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL J 316 " --> pdb=" O ILE J 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 1531 hydrogen bonds defined for protein. 4485 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.42 Time building geometry restraints manager: 9.67 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: 7885 1.34 - 1.45: 3036 1.45 - 1.57: 13116 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 24141 Sorted by residual: bond pdb=" C LEU A 270 " pdb=" N ASN A 271 " ideal model delta sigma weight residual 1.327 1.246 0.081 2.31e-02 1.87e+03 1.23e+01 bond pdb=" N VAL G 350 " pdb=" CA VAL G 350 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.92e+00 bond pdb=" N LEU G 349 " pdb=" CA LEU G 349 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.90e+00 bond pdb=" N ARG C 312 " pdb=" CA ARG C 312 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.41e-02 5.03e+03 6.75e+00 bond pdb=" N SER G 351 " pdb=" CA SER G 351 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.22e-02 6.72e+03 6.00e+00 ... (remaining 24136 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.74: 737 105.74 - 112.84: 14013 112.84 - 119.93: 7508 119.93 - 127.03: 10420 127.03 - 134.13: 423 Bond angle restraints: 33101 Sorted by residual: angle pdb=" N ILE E 328 " pdb=" CA ILE E 328 " pdb=" C ILE E 328 " ideal model delta sigma weight residual 113.71 107.40 6.31 9.50e-01 1.11e+00 4.41e+01 angle pdb=" N ARG J 151 " pdb=" CA ARG J 151 " pdb=" C ARG J 151 " ideal model delta sigma weight residual 114.64 105.58 9.06 1.52e+00 4.33e-01 3.55e+01 angle pdb=" N ILE J 328 " pdb=" CA ILE J 328 " pdb=" C ILE J 328 " ideal model delta sigma weight residual 111.62 108.19 3.43 7.90e-01 1.60e+00 1.88e+01 angle pdb=" N ASP H 19 " pdb=" CA ASP H 19 " pdb=" C ASP H 19 " ideal model delta sigma weight residual 114.39 108.40 5.99 1.45e+00 4.76e-01 1.71e+01 angle pdb=" N TRP E 258 " pdb=" CA TRP E 258 " pdb=" C TRP E 258 " ideal model delta sigma weight residual 114.64 108.46 6.18 1.52e+00 4.33e-01 1.66e+01 ... (remaining 33096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13337 17.86 - 35.71: 913 35.71 - 53.57: 130 53.57 - 71.43: 43 71.43 - 89.28: 24 Dihedral angle restraints: 14447 sinusoidal: 5342 harmonic: 9105 Sorted by residual: dihedral pdb=" CA SER D 15 " pdb=" C SER D 15 " pdb=" N ARG D 16 " pdb=" CA ARG D 16 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ARG E 349 " pdb=" C ARG E 349 " pdb=" N GLU E 350 " pdb=" CA GLU E 350 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASP E 364 " pdb=" C ASP E 364 " pdb=" N GLY E 365 " pdb=" CA GLY E 365 " ideal model delta harmonic sigma weight residual 180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 14444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3260 0.053 - 0.106: 689 0.106 - 0.159: 104 0.159 - 0.212: 5 0.212 - 0.265: 1 Chirality restraints: 4059 Sorted by residual: chirality pdb=" CB ILE H 459 " pdb=" CA ILE H 459 " pdb=" CG1 ILE H 459 " pdb=" CG2 ILE H 459 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE J 180 " pdb=" CA ILE J 180 " pdb=" CG1 ILE J 180 " pdb=" CG2 ILE J 180 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL C 167 " pdb=" CA VAL C 167 " pdb=" CG1 VAL C 167 " pdb=" CG2 VAL C 167 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 4056 not shown) Planarity restraints: 4231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 200 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.47e+00 pdb=" C VAL E 200 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL E 200 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG E 201 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 435 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO H 436 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 436 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 436 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 441 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO C 442 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 442 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 442 " -0.026 5.00e-02 4.00e+02 ... (remaining 4228 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3222 2.74 - 3.28: 24920 3.28 - 3.82: 39502 3.82 - 4.36: 44139 4.36 - 4.90: 76758 Nonbonded interactions: 188541 Sorted by model distance: nonbonded pdb=" OG SER C 352 " pdb=" OD1 ASN C 354 " model vdw 2.203 2.440 nonbonded pdb=" O THR C 82 " pdb=" OG1 THR C 85 " model vdw 2.227 2.440 nonbonded pdb=" NH1 ARG J 225 " pdb=" OD2 ASP J 257 " model vdw 2.230 2.520 nonbonded pdb=" OG SER G 31 " pdb=" OD1 ASP G 84 " model vdw 2.231 2.440 nonbonded pdb=" NE ARG A 138 " pdb=" OE2 GLU C 110 " model vdw 2.237 2.520 ... (remaining 188536 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 'F' } ncs_group { reference = (chain 'B' and (resid 7 through 49 or resid 67 through 475)) selection = (chain 'C' and (resid 7 through 295 or resid 313 through 475)) selection = (chain 'G' and (resid 7 through 49 or resid 67 through 475)) selection = (chain 'H' and (resid 7 through 295 or resid 313 through 475)) } ncs_group { reference = chain 'E' selection = chain 'J' } 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=0.00 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.360 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 60.630 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.130 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 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 : 0.006 0.081 24141 Z= 0.429 Angle : 0.793 13.638 33101 Z= 0.455 Chirality : 0.043 0.265 4059 Planarity : 0.005 0.046 4231 Dihedral : 13.227 89.283 8539 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.17 % Allowed : 7.66 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.13), residues: 3148 helix: -0.54 (0.11), residues: 1748 sheet: -2.31 (0.25), residues: 283 loop : -2.33 (0.16), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 293 HIS 0.008 0.002 HIS J 239 PHE 0.020 0.002 PHE I 88 TYR 0.027 0.002 TYR F 96 ARG 0.007 0.001 ARG J 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 599 time to evaluate : 2.469 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 600 average time/residue: 0.3470 time to fit residues: 330.9795 Evaluate side-chains 367 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 366 time to evaluate : 2.814 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.8328 time to fit residues: 4.6817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 247 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 89 GLN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 HIS ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN C 154 HIS C 216 ASN C 328 GLN E 130 HIS E 187 HIS ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN E 313 HIS F 74 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN G 47 GLN G 328 GLN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 GLN ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 313 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24141 Z= 0.240 Angle : 0.732 9.977 33101 Z= 0.355 Chirality : 0.045 0.342 4059 Planarity : 0.005 0.045 4231 Dihedral : 4.836 73.726 3452 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.35 % Allowed : 18.05 % Favored : 78.60 % 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: -0.47 (0.15), residues: 3148 helix: 0.68 (0.12), residues: 1763 sheet: -1.81 (0.27), residues: 288 loop : -1.43 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 231 HIS 0.007 0.001 HIS G 389 PHE 0.029 0.002 PHE G 165 TYR 0.026 0.002 TYR F 96 ARG 0.010 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 398 time to evaluate : 2.628 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 37 residues processed: 443 average time/residue: 0.3084 time to fit residues: 223.8104 Evaluate side-chains 366 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 329 time to evaluate : 2.633 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2302 time to fit residues: 18.7717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 40.0000 chunk 89 optimal weight: 7.9990 chunk 238 optimal weight: 30.0000 chunk 195 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 chunk 287 optimal weight: 6.9990 chunk 310 optimal weight: 30.0000 chunk 256 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 HIS H 285 GLN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 408 GLN ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 24141 Z= 0.344 Angle : 0.781 11.624 33101 Z= 0.385 Chirality : 0.044 0.262 4059 Planarity : 0.005 0.052 4231 Dihedral : 4.795 69.792 3452 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.23 % Allowed : 21.19 % Favored : 75.58 % 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: -0.09 (0.15), residues: 3148 helix: 0.93 (0.12), residues: 1772 sheet: -1.73 (0.27), residues: 290 loop : -1.13 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP E 231 HIS 0.007 0.001 HIS G 389 PHE 0.036 0.002 PHE C 244 TYR 0.023 0.002 TYR F 96 ARG 0.008 0.001 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 346 time to evaluate : 2.732 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 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: 78 outliers final: 33 residues processed: 394 average time/residue: 0.2835 time to fit residues: 186.7694 Evaluate side-chains 349 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 316 time to evaluate : 2.436 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2064 time to fit residues: 16.2631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 0.2980 chunk 216 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 288 optimal weight: 3.9990 chunk 305 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN C 126 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 GLN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24141 Z= 0.210 Angle : 0.741 13.638 33101 Z= 0.345 Chirality : 0.044 0.346 4059 Planarity : 0.004 0.050 4231 Dihedral : 4.684 67.269 3452 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.24 % Allowed : 23.14 % Favored : 74.63 % 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: 0.33 (0.15), residues: 3148 helix: 1.23 (0.12), residues: 1767 sheet: -1.55 (0.27), residues: 294 loop : -0.87 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 231 HIS 0.006 0.001 HIS G 389 PHE 0.047 0.002 PHE C 401 TYR 0.021 0.002 TYR F 96 ARG 0.011 0.000 ARG I 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 347 time to evaluate : 2.547 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 23 residues processed: 379 average time/residue: 0.2957 time to fit residues: 188.2652 Evaluate side-chains 328 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 305 time to evaluate : 2.579 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2193 time to fit residues: 12.6813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 69.1994 > 50: distance: 59 - 63: 30.194 distance: 63 - 64: 3.560 distance: 64 - 65: 9.991 distance: 64 - 67: 30.956 distance: 65 - 66: 39.586 distance: 68 - 69: 42.083 distance: 69 - 70: 32.869 distance: 69 - 72: 40.929 distance: 70 - 71: 10.129 distance: 70 - 79: 29.172 distance: 72 - 73: 12.282 distance: 75 - 76: 3.277 distance: 76 - 77: 37.540 distance: 76 - 78: 31.249 distance: 80 - 81: 67.584 distance: 80 - 83: 33.983 distance: 81 - 82: 37.771 distance: 81 - 87: 56.467 distance: 83 - 84: 26.765 distance: 83 - 85: 21.015 distance: 84 - 86: 28.215 distance: 87 - 88: 58.703 distance: 87 - 93: 50.180 distance: 88 - 89: 49.805 distance: 88 - 91: 43.737 distance: 89 - 90: 21.777 distance: 89 - 94: 11.942 distance: 90 - 119: 41.189 distance: 91 - 92: 17.173 distance: 92 - 93: 37.266 distance: 94 - 95: 38.551 distance: 95 - 96: 20.673 distance: 95 - 98: 27.149 distance: 96 - 97: 36.020 distance: 96 - 102: 20.814 distance: 97 - 126: 43.216 distance: 98 - 99: 9.864 distance: 99 - 100: 4.077 distance: 99 - 101: 24.296 distance: 103 - 104: 19.264 distance: 103 - 106: 7.743 distance: 104 - 105: 17.282 distance: 104 - 111: 51.375 distance: 105 - 133: 3.313 distance: 106 - 107: 10.587 distance: 107 - 108: 41.635 distance: 108 - 109: 20.726 distance: 108 - 110: 12.635 distance: 111 - 112: 41.524 distance: 112 - 113: 43.609 distance: 112 - 115: 7.544 distance: 113 - 114: 36.396 distance: 113 - 119: 39.931 distance: 114 - 142: 28.786 distance: 115 - 116: 26.526 distance: 116 - 117: 27.783 distance: 116 - 118: 19.321 distance: 119 - 120: 39.653 distance: 120 - 121: 8.857 distance: 120 - 123: 18.385 distance: 121 - 122: 10.860 distance: 121 - 126: 18.233 distance: 122 - 149: 26.321 distance: 126 - 127: 32.405 distance: 127 - 128: 20.199 distance: 127 - 130: 26.725 distance: 128 - 129: 19.088 distance: 128 - 133: 31.462 distance: 129 - 156: 27.453 distance: 130 - 131: 32.930 distance: 130 - 132: 16.943 distance: 133 - 134: 21.464 distance: 134 - 135: 28.012 distance: 134 - 137: 38.637 distance: 135 - 136: 16.734 distance: 135 - 142: 28.502 distance: 136 - 160: 34.816 distance: 137 - 138: 41.432 distance: 138 - 139: 39.289 distance: 139 - 140: 4.814 distance: 139 - 141: 14.378