Starting phenix.real_space_refine on Thu Jan 18 18:57:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmk_0917/01_2024/6lmk_0917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmk_0917/01_2024/6lmk_0917.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/6lmk_0917/01_2024/6lmk_0917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmk_0917/01_2024/6lmk_0917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmk_0917/01_2024/6lmk_0917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmk_0917/01_2024/6lmk_0917.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= 0.002 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 58 5.16 5 C 5863 2.51 5 N 1631 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 133": "OE1" <-> "OE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 195": "OD1" <-> "OD2" Residue "R ASP 209": "OD1" <-> "OD2" Residue "R GLU 260": "OE1" <-> "OE2" Residue "R PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9240 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1889 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2584 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 420 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3138 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "E" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 245 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Time building chain proxies: 5.39, per 1000 atoms: 0.58 Number of scatterers: 9240 At special positions: 0 Unit cell: (97.58, 163.18, 86.92, 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 58 16.00 O 1688 8.00 N 1631 7.00 C 5863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.03 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.04 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.8 seconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 11 sheets defined 39.9% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 4.404A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.986A pdb=" N THR A 55 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 56' Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.789A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.907A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.634A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.729A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.659A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 25 removed outlier: 4.253A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.547A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 8 through 24 removed outlier: 4.455A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'N' and resid 61 through 65 removed outlier: 3.608A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.050A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 48 Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'R' and resid 117 through 122 removed outlier: 4.487A pdb=" N GLN R 120 " --> pdb=" O ASP R 117 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS R 121 " --> pdb=" O ALA R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 164 removed outlier: 3.882A pdb=" N LEU R 151 " --> pdb=" O VAL R 147 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU R 158 " --> pdb=" O GLY R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 202 removed outlier: 3.588A pdb=" N HIS R 177 " --> pdb=" O ARG R 173 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER R 183 " --> pdb=" O ASN R 179 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER R 190 " --> pdb=" O LEU R 186 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 217 Processing helix chain 'R' and resid 220 through 251 removed outlier: 3.759A pdb=" N CYS R 224 " --> pdb=" O ALA R 220 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL R 236 " --> pdb=" O GLN R 232 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR R 239 " --> pdb=" O ILE R 235 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU R 249 " --> pdb=" O GLU R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 273 Processing helix chain 'R' and resid 273 through 289 Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 304 through 333 Proline residue: R 310 - end of helix removed outlier: 4.879A pdb=" N ASN R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL R 326 " --> pdb=" O PHE R 322 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU R 328 " --> pdb=" O ARG R 324 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA R 331 " --> pdb=" O GLN R 327 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 347 Processing helix chain 'R' and resid 374 through 402 removed outlier: 3.535A pdb=" N ARG R 378 " --> pdb=" O GLN R 374 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 419 removed outlier: 3.565A pdb=" N ARG R 414 " --> pdb=" O GLU R 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.853A pdb=" N THR E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER E 8 " --> pdb=" O GLY E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 29 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 4.031A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.577A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.943A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.503A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.854A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.571A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.070A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.585A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.667A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 75 through 80 removed outlier: 3.539A pdb=" N THR R 75 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS R 98 " --> pdb=" O ALA R 77 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 3.96 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: 2936 1.34 - 1.46: 2091 1.46 - 1.58: 4340 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 9447 Sorted by residual: bond pdb=" CG1 ILE R 321 " pdb=" CD1 ILE R 321 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.58e+00 bond pdb=" CB TRP R 241 " pdb=" CG TRP R 241 " ideal model delta sigma weight residual 1.498 1.429 0.069 3.10e-02 1.04e+03 4.94e+00 bond pdb=" CB ILE R 355 " pdb=" CG2 ILE R 355 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.43e+00 bond pdb=" CB ASN A 239 " pdb=" CG ASN A 239 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.34e+00 bond pdb=" CB VAL B 315 " pdb=" CG2 VAL B 315 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.73e+00 ... (remaining 9442 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.14: 179 106.14 - 113.14: 5065 113.14 - 120.14: 3581 120.14 - 127.14: 3865 127.14 - 134.13: 120 Bond angle restraints: 12810 Sorted by residual: angle pdb=" CA TYR R 145 " pdb=" CB TYR R 145 " pdb=" CG TYR R 145 " ideal model delta sigma weight residual 113.90 120.39 -6.49 1.80e+00 3.09e-01 1.30e+01 angle pdb=" C GLN R 42 " pdb=" N CYS R 43 " pdb=" CA CYS R 43 " ideal model delta sigma weight residual 122.06 115.58 6.48 1.86e+00 2.89e-01 1.21e+01 angle pdb=" N VAL R 280 " pdb=" CA VAL R 280 " pdb=" C VAL R 280 " ideal model delta sigma weight residual 108.88 116.30 -7.42 2.16e+00 2.14e-01 1.18e+01 angle pdb=" N GLY R 302 " pdb=" CA GLY R 302 " pdb=" C GLY R 302 " ideal model delta sigma weight residual 111.15 105.43 5.72 1.76e+00 3.23e-01 1.06e+01 angle pdb=" CA ILE R 355 " pdb=" C ILE R 355 " pdb=" N PRO R 356 " ideal model delta sigma weight residual 118.88 123.73 -4.85 1.54e+00 4.22e-01 9.93e+00 ... (remaining 12805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4945 17.94 - 35.88: 523 35.88 - 53.82: 105 53.82 - 71.76: 12 71.76 - 89.70: 7 Dihedral angle restraints: 5592 sinusoidal: 2176 harmonic: 3416 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 5.98 87.02 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CA CYS R 58 " pdb=" C CYS R 58 " pdb=" N ASN R 59 " pdb=" CA ASN R 59 " ideal model delta harmonic sigma weight residual 180.00 -141.89 -38.11 0 5.00e+00 4.00e-02 5.81e+01 dihedral pdb=" CA PHE R 303 " pdb=" C PHE R 303 " pdb=" N TRP R 304 " pdb=" CA TRP R 304 " ideal model delta harmonic sigma weight residual 180.00 142.15 37.85 0 5.00e+00 4.00e-02 5.73e+01 ... (remaining 5589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 977 0.055 - 0.109: 350 0.109 - 0.164: 75 0.164 - 0.218: 15 0.218 - 0.273: 2 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB ILE N 70 " pdb=" CA ILE N 70 " pdb=" CG1 ILE N 70 " pdb=" CG2 ILE N 70 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB VAL R 280 " pdb=" CA VAL R 280 " pdb=" CG1 VAL R 280 " pdb=" CG2 VAL R 280 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1416 not shown) Planarity restraints: 1641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 355 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO R 356 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO R 356 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 356 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO B 236 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 63 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C ASP R 63 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP R 63 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS R 64 " -0.015 2.00e-02 2.50e+03 ... (remaining 1638 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2835 2.81 - 3.33: 8440 3.33 - 3.85: 15588 3.85 - 4.38: 17632 4.38 - 4.90: 30462 Nonbonded interactions: 74957 Sorted by model distance: nonbonded pdb=" OH TYR R 145 " pdb=" OD2 ASP R 195 " model vdw 2.283 2.440 nonbonded pdb=" OG SER A 251 " pdb=" O LYS A 293 " model vdw 2.297 2.440 nonbonded pdb=" O SER R 189 " pdb=" OG SER R 189 " model vdw 2.312 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" OD1 ASP B 290 " model vdw 2.313 2.440 nonbonded pdb=" NE1 TRP N 47 " pdb=" O SER N 49 " model vdw 2.320 2.520 ... (remaining 74952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.870 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: 0.000 Extract box with map and model: 4.110 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 27.370 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.009 0.114 9447 Z= 0.565 Angle : 0.960 9.616 12810 Z= 0.522 Chirality : 0.058 0.273 1419 Planarity : 0.007 0.074 1641 Dihedral : 15.097 89.701 3366 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.62 % Allowed : 10.36 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.20), residues: 1162 helix: -2.62 (0.18), residues: 420 sheet: -2.88 (0.31), residues: 189 loop : -2.80 (0.22), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP R 241 HIS 0.013 0.002 HIS R 361 PHE 0.032 0.003 PHE N 108 TYR 0.036 0.003 TYR B 59 ARG 0.005 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 201 time to evaluate : 1.163 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: A 32 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8283 (mtmm) REVERT: A 265 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7002 (ttm110) REVERT: A 344 GLU cc_start: 0.8015 (tp30) cc_final: 0.7789 (tp30) REVERT: B 169 TRP cc_start: 0.8671 (m100) cc_final: 0.8397 (m100) REVERT: B 270 ILE cc_start: 0.8485 (tp) cc_final: 0.8216 (tp) REVERT: B 291 ASP cc_start: 0.8426 (p0) cc_final: 0.8205 (p0) REVERT: C 17 GLU cc_start: 0.7923 (tp30) cc_final: 0.7601 (tp30) REVERT: C 50 LEU cc_start: 0.8880 (mm) cc_final: 0.8503 (mm) REVERT: N 38 ARG cc_start: 0.8542 (ptt180) cc_final: 0.7916 (ptt90) REVERT: N 91 THR cc_start: 0.8621 (p) cc_final: 0.8364 (p) REVERT: R 123 MET cc_start: 0.7719 (mmm) cc_final: 0.7372 (mmm) REVERT: R 127 GLU cc_start: 0.8645 (mp0) cc_final: 0.8195 (mp0) REVERT: R 133 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8073 (tp30) REVERT: R 270 ILE cc_start: 0.9062 (tt) cc_final: 0.8838 (tt) REVERT: R 410 GLU cc_start: 0.7758 (tp30) cc_final: 0.7448 (tp30) REVERT: E 15 ASP cc_start: 0.8414 (p0) cc_final: 0.7991 (p0) REVERT: E 17 ARG cc_start: 0.8664 (tpt90) cc_final: 0.7984 (tpp80) REVERT: E 21 ASP cc_start: 0.8596 (m-30) cc_final: 0.8222 (m-30) REVERT: E 24 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8678 (tm-30) outliers start: 6 outliers final: 1 residues processed: 207 average time/residue: 0.2555 time to fit residues: 69.3211 Evaluate side-chains 152 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.0050 chunk 58 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 66 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 31 GLN A 267 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 230 ASN B 293 ASN B 295 ASN C 11 GLN N 31 ASN ** R 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 ASN R 404 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9447 Z= 0.156 Angle : 0.589 8.920 12810 Z= 0.306 Chirality : 0.041 0.144 1419 Planarity : 0.004 0.060 1641 Dihedral : 5.616 36.706 1285 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.56 % Allowed : 16.62 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.69 (0.23), residues: 1162 helix: -0.48 (0.24), residues: 416 sheet: -2.78 (0.30), residues: 219 loop : -2.37 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 241 HIS 0.007 0.001 HIS R 361 PHE 0.021 0.001 PHE B 235 TYR 0.021 0.001 TYR R 145 ARG 0.002 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.6928 (ttm-80) REVERT: A 317 ARG cc_start: 0.7620 (ttp-110) cc_final: 0.7290 (ptt180) REVERT: B 264 TYR cc_start: 0.8060 (m-80) cc_final: 0.6952 (m-80) REVERT: B 270 ILE cc_start: 0.8195 (tp) cc_final: 0.7937 (tp) REVERT: C 51 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8595 (mp) REVERT: N 5 GLN cc_start: 0.8118 (mp10) cc_final: 0.7841 (mp10) REVERT: N 51 ILE cc_start: 0.8900 (tt) cc_final: 0.8634 (tt) REVERT: N 72 ARG cc_start: 0.8210 (ptm160) cc_final: 0.7904 (ptm160) REVERT: R 123 MET cc_start: 0.7711 (mmm) cc_final: 0.7416 (mmm) REVERT: R 127 GLU cc_start: 0.8583 (mp0) cc_final: 0.7877 (mp0) REVERT: R 133 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8084 (tp30) REVERT: R 231 MET cc_start: 0.7536 (tmm) cc_final: 0.7042 (ttm) REVERT: E 12 LYS cc_start: 0.9166 (mtmt) cc_final: 0.8857 (mtmm) REVERT: E 15 ASP cc_start: 0.8362 (p0) cc_final: 0.8150 (p0) REVERT: E 17 ARG cc_start: 0.8641 (tpt90) cc_final: 0.8242 (tpp80) REVERT: E 21 ASP cc_start: 0.8504 (m-30) cc_final: 0.8189 (m-30) REVERT: E 24 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8684 (tm-30) REVERT: E 27 MET cc_start: 0.8301 (mmp) cc_final: 0.7815 (mmm) outliers start: 25 outliers final: 14 residues processed: 210 average time/residue: 0.2384 time to fit residues: 67.0705 Evaluate side-chains 182 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 102 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9447 Z= 0.313 Angle : 0.644 7.442 12810 Z= 0.336 Chirality : 0.043 0.159 1419 Planarity : 0.004 0.054 1641 Dihedral : 5.488 37.850 1285 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.10 % Allowed : 19.90 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.01 (0.24), residues: 1162 helix: 0.29 (0.26), residues: 415 sheet: -2.41 (0.32), residues: 208 loop : -2.18 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.007 0.001 HIS R 361 PHE 0.020 0.002 PHE N 108 TYR 0.021 0.002 TYR R 145 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 171 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8360 (tttt) cc_final: 0.8052 (mmtm) REVERT: A 35 GLN cc_start: 0.8089 (tt0) cc_final: 0.7884 (mt0) REVERT: A 265 ARG cc_start: 0.7754 (ttm-80) cc_final: 0.7115 (ttm110) REVERT: B 82 TRP cc_start: 0.8714 (m100) cc_final: 0.8206 (m100) REVERT: B 264 TYR cc_start: 0.8182 (m-80) cc_final: 0.7280 (m-80) REVERT: B 270 ILE cc_start: 0.8315 (tp) cc_final: 0.8023 (tp) REVERT: C 51 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8703 (mp) REVERT: N 5 GLN cc_start: 0.8235 (mp10) cc_final: 0.7990 (mp10) REVERT: N 38 ARG cc_start: 0.8482 (ptt90) cc_final: 0.8153 (ptm-80) REVERT: N 51 ILE cc_start: 0.9036 (tt) cc_final: 0.8739 (tt) REVERT: N 76 LYS cc_start: 0.9109 (mmmm) cc_final: 0.8648 (tptt) REVERT: R 123 MET cc_start: 0.7861 (mmm) cc_final: 0.7515 (mmm) REVERT: R 133 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8138 (tp30) REVERT: E 12 LYS cc_start: 0.9228 (mtmt) cc_final: 0.9005 (mtmm) REVERT: E 15 ASP cc_start: 0.8530 (p0) cc_final: 0.8293 (p0) REVERT: E 17 ARG cc_start: 0.8704 (tpt90) cc_final: 0.8215 (tpp80) REVERT: E 21 ASP cc_start: 0.8665 (m-30) cc_final: 0.8283 (m-30) REVERT: E 24 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8639 (tm-30) REVERT: E 27 MET cc_start: 0.8256 (mmp) cc_final: 0.7609 (mmm) outliers start: 40 outliers final: 30 residues processed: 198 average time/residue: 0.2491 time to fit residues: 65.7419 Evaluate side-chains 189 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 64 LYS Chi-restraints excluded: chain R residue 65 TYR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 330 VAL Chi-restraints excluded: chain R residue 351 THR Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 213 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS C 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9447 Z= 0.154 Angle : 0.556 8.848 12810 Z= 0.285 Chirality : 0.040 0.142 1419 Planarity : 0.003 0.049 1641 Dihedral : 4.928 35.682 1285 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.67 % Allowed : 22.46 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.25), residues: 1162 helix: 0.86 (0.26), residues: 418 sheet: -2.36 (0.31), residues: 229 loop : -1.91 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 241 HIS 0.006 0.001 HIS R 361 PHE 0.012 0.001 PHE R 384 TYR 0.017 0.001 TYR R 145 ARG 0.003 0.000 ARG R 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8302 (tttt) cc_final: 0.8050 (mmtm) REVERT: A 265 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7043 (ttm110) REVERT: A 364 THR cc_start: 0.8185 (p) cc_final: 0.7952 (p) REVERT: A 390 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: B 82 TRP cc_start: 0.8579 (m100) cc_final: 0.8079 (m100) REVERT: B 264 TYR cc_start: 0.8073 (m-80) cc_final: 0.7204 (m-80) REVERT: C 51 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8679 (mp) REVERT: N 51 ILE cc_start: 0.8717 (tt) cc_final: 0.8344 (tt) REVERT: N 53 GLN cc_start: 0.8236 (mp10) cc_final: 0.7941 (mp10) REVERT: N 72 ARG cc_start: 0.8349 (ptm160) cc_final: 0.7918 (ptm160) REVERT: N 76 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8612 (tptt) REVERT: N 94 TYR cc_start: 0.8597 (m-80) cc_final: 0.8295 (m-80) REVERT: R 123 MET cc_start: 0.7996 (mmm) cc_final: 0.7729 (mmm) REVERT: R 126 GLU cc_start: 0.7815 (pm20) cc_final: 0.7613 (pm20) REVERT: R 127 GLU cc_start: 0.8388 (mp0) cc_final: 0.7516 (mp0) REVERT: R 133 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8164 (tp30) REVERT: R 231 MET cc_start: 0.7613 (tmm) cc_final: 0.6971 (ttm) REVERT: R 301 MET cc_start: 0.8084 (ppp) cc_final: 0.7661 (ppp) REVERT: E 12 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8811 (mtmm) REVERT: E 15 ASP cc_start: 0.8378 (p0) cc_final: 0.8089 (p0) REVERT: E 17 ARG cc_start: 0.8663 (tpt90) cc_final: 0.8165 (tpp80) REVERT: E 21 ASP cc_start: 0.8695 (m-30) cc_final: 0.8432 (m-30) REVERT: E 24 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8729 (tm-30) REVERT: E 27 MET cc_start: 0.8214 (mmp) cc_final: 0.7551 (mmm) outliers start: 26 outliers final: 18 residues processed: 196 average time/residue: 0.2568 time to fit residues: 66.1997 Evaluate side-chains 174 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 64 LYS Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 351 THR Chi-restraints excluded: chain R residue 363 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 55.073 > 50: distance: 6 - 8: 24.632 distance: 8 - 9: 36.930 distance: 9 - 10: 9.141 distance: 10 - 11: 29.055 distance: 10 - 12: 39.345 distance: 12 - 13: 8.353 distance: 13 - 14: 20.719 distance: 13 - 16: 18.411 distance: 14 - 15: 18.795 distance: 14 - 20: 10.965 distance: 16 - 17: 24.622 distance: 17 - 18: 33.397 distance: 17 - 19: 40.013 distance: 20 - 21: 15.685 distance: 20 - 143: 21.658 distance: 21 - 22: 12.476 distance: 21 - 24: 20.720 distance: 22 - 23: 30.711 distance: 22 - 27: 12.131 distance: 24 - 25: 29.504 distance: 24 - 26: 18.701 distance: 27 - 28: 18.145 distance: 28 - 29: 19.679 distance: 28 - 31: 6.985 distance: 29 - 30: 3.415 distance: 29 - 36: 14.181 distance: 31 - 32: 20.828 distance: 32 - 33: 12.708 distance: 33 - 34: 4.071 distance: 33 - 35: 6.701 distance: 36 - 37: 8.018 distance: 36 - 42: 9.676 distance: 37 - 38: 4.057 distance: 37 - 40: 20.893 distance: 38 - 39: 11.038 distance: 38 - 43: 11.470 distance: 40 - 41: 35.851 distance: 41 - 42: 6.298 distance: 43 - 44: 7.713 distance: 44 - 45: 5.589 distance: 45 - 46: 18.982 distance: 45 - 47: 16.180 distance: 47 - 48: 22.930 distance: 48 - 49: 16.396 distance: 49 - 50: 26.314 distance: 49 - 51: 20.763 distance: 51 - 52: 5.243 distance: 52 - 53: 3.602 distance: 52 - 55: 13.071 distance: 53 - 54: 5.925 distance: 53 - 57: 15.553 distance: 55 - 56: 30.044 distance: 57 - 58: 20.461 distance: 58 - 59: 9.345 distance: 58 - 61: 11.954 distance: 59 - 60: 20.679 distance: 59 - 65: 16.918 distance: 61 - 62: 30.719 distance: 62 - 63: 32.120 distance: 62 - 64: 25.617 distance: 65 - 66: 4.440 distance: 66 - 67: 16.263 distance: 66 - 69: 15.711 distance: 67 - 68: 3.796 distance: 67 - 76: 23.481 distance: 69 - 70: 26.873 distance: 70 - 71: 28.779 distance: 71 - 72: 6.847 distance: 73 - 74: 5.557 distance: 73 - 75: 8.121