Starting phenix.real_space_refine on Sat Aug 3 21:34:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpf_0744/08_2024/6kpf_0744.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpf_0744/08_2024/6kpf_0744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpf_0744/08_2024/6kpf_0744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpf_0744/08_2024/6kpf_0744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpf_0744/08_2024/6kpf_0744.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpf_0744/08_2024/6kpf_0744.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 66 5.16 5 C 5599 2.51 5 N 1493 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "R ARG 65": "NH1" <-> "NH2" Residue "R ARG 66": "NH1" <-> "NH2" Residue "R ASP 80": "OD1" <-> "OD2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R ARG 136": "NH1" <-> "NH2" Residue "R ARG 147": "NH1" <-> "NH2" Residue "R ARG 149": "NH1" <-> "NH2" Residue "R PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 189": "OD1" <-> "OD2" Residue "R ARG 238": "NH1" <-> "NH2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "S ARG 98": "NH1" <-> "NH2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 206": "NH1" <-> "NH2" Residue "S GLU 208": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8775 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1708 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2250 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'E3R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.61 Number of scatterers: 8775 At special positions: 0 Unit cell: (118.56, 100.88, 120.64, 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 66 16.00 O 1617 8.00 N 1493 7.00 C 5599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 3.40 Conformation dependent library (CDL) restraints added in 1.7 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 34.9% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.514A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.505A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.919A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.936A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.757A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.543A 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 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.724A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.717A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'R' and resid 30 through 61 removed outlier: 4.424A pdb=" N LEU R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL R 52 " --> pdb=" O ALA R 48 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU R 59 " --> pdb=" O LEU R 55 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 66 removed outlier: 3.602A pdb=" N ARG R 66 " --> pdb=" O HIS R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 86 Processing helix chain 'R' and resid 86 through 96 removed outlier: 3.638A pdb=" N VAL R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE R 94 " --> pdb=" O SER R 90 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL R 96 " --> pdb=" O VAL R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 131 removed outlier: 3.840A pdb=" N THR R 116 " --> pdb=" O SER R 112 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER R 120 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.522A pdb=" N THR R 153 " --> pdb=" O ARG R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 216 removed outlier: 3.811A pdb=" N SER R 193 " --> pdb=" O ASP R 189 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR R 207 " --> pdb=" O SER R 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 224 Processing helix chain 'R' and resid 238 through 245 Processing helix chain 'R' and resid 245 through 254 removed outlier: 3.608A pdb=" N LEU R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL R 253 " --> pdb=" O LEU R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 263 Processing helix chain 'R' and resid 265 through 269 removed outlier: 3.946A pdb=" N SER R 268 " --> pdb=" O MET R 265 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU R 269 " --> pdb=" O ALA R 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 265 through 269' Processing helix chain 'R' and resid 279 through 285 Processing helix chain 'R' and resid 286 through 291 Processing helix chain 'R' and resid 294 through 300 Processing helix chain 'R' and resid 303 through 311 removed outlier: 3.586A pdb=" N ARG R 307 " --> pdb=" O SER R 303 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER R 309 " --> pdb=" O GLU R 305 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.754A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.525A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.718A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.918A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.083A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.374A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.668A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.655A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.230A 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: 3.558A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.625A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.739A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.213A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.579A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 143 through 148 393 hydrogen bonds defined for protein. 1098 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: 2.98 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1401 1.29 - 1.43: 2404 1.43 - 1.57: 5061 1.57 - 1.70: 1 1.70 - 1.84: 95 Bond restraints: 8962 Sorted by residual: bond pdb=" CA ILE R 186 " pdb=" CB ILE R 186 " ideal model delta sigma weight residual 1.537 1.565 -0.028 1.29e-02 6.01e+03 4.74e+00 bond pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.22e+00 bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.17e+00 bond pdb=" C LEU R 167 " pdb=" N PRO R 168 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.40e+00 bond pdb=" C4 E3R R 401 " pdb=" C5 E3R R 401 " ideal model delta sigma weight residual 1.399 1.435 -0.036 2.00e-02 2.50e+03 3.28e+00 ... (remaining 8957 not shown) Histogram of bond angle deviations from ideal: 99.21 - 114.91: 5591 114.91 - 130.61: 6506 130.61 - 146.32: 51 146.32 - 162.02: 0 162.02 - 177.72: 1 Bond angle restraints: 12149 Sorted by residual: angle pdb=" CA CYS R 179 " pdb=" CB CYS R 179 " pdb=" SG CYS R 179 " ideal model delta sigma weight residual 114.40 126.55 -12.15 2.30e+00 1.89e-01 2.79e+01 angle pdb=" C PRO R 178 " pdb=" N CYS R 179 " pdb=" CA CYS R 179 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C11 E3R R 401 " pdb=" C10 E3R R 401 " pdb=" C7 E3R R 401 " ideal model delta sigma weight residual 111.05 124.27 -13.22 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta sigma weight residual 122.03 113.59 8.44 2.01e+00 2.48e-01 1.76e+01 angle pdb=" C3 E3R R 401 " pdb=" C4 E3R R 401 " pdb=" O3 E3R R 401 " ideal model delta sigma weight residual 120.37 108.10 12.27 3.00e+00 1.11e-01 1.67e+01 ... (remaining 12144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 4759 18.06 - 36.12: 469 36.12 - 54.18: 84 54.18 - 72.24: 12 72.24 - 90.30: 9 Dihedral angle restraints: 5333 sinusoidal: 2049 harmonic: 3284 Sorted by residual: dihedral pdb=" CA PRO R 178 " pdb=" C PRO R 178 " pdb=" N CYS R 179 " pdb=" CA CYS R 179 " ideal model delta harmonic sigma weight residual 180.00 124.09 55.91 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CB CYS R 174 " pdb=" SG CYS R 174 " pdb=" SG CYS R 179 " pdb=" CB CYS R 179 " ideal model delta sinusoidal sigma weight residual -86.00 -6.95 -79.05 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 5330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1126 0.063 - 0.126: 229 0.126 - 0.189: 27 0.189 - 0.252: 6 0.252 - 0.315: 2 Chirality restraints: 1390 Sorted by residual: chirality pdb=" C11 E3R R 401 " pdb=" C10 E3R R 401 " pdb=" C12 E3R R 401 " pdb=" C14 E3R R 401 " both_signs ideal model delta sigma weight residual False -2.57 -2.89 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C8 E3R R 401 " pdb=" C13 E3R R 401 " pdb=" C7 E3R R 401 " pdb=" C9 E3R R 401 " both_signs ideal model delta sigma weight residual False 2.42 2.73 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1387 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO R 168 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 259 " -0.046 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO R 260 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO R 260 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 260 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 186 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO R 187 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 187 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 187 " -0.036 5.00e-02 4.00e+02 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1268 2.75 - 3.29: 7769 3.29 - 3.83: 15111 3.83 - 4.36: 18525 4.36 - 4.90: 31676 Nonbonded interactions: 74349 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ARG B 129 " model vdw 2.215 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.235 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.245 3.040 nonbonded pdb=" O SER R 161 " pdb=" OG SER R 165 " model vdw 2.258 3.040 ... (remaining 74344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.590 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 8962 Z= 0.445 Angle : 0.909 13.222 12149 Z= 0.468 Chirality : 0.054 0.315 1390 Planarity : 0.007 0.091 1521 Dihedral : 14.925 90.302 3206 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.39 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.46 (0.20), residues: 1117 helix: -4.64 (0.09), residues: 384 sheet: -1.43 (0.28), residues: 285 loop : -2.14 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.005 0.001 HIS A 188 PHE 0.020 0.002 PHE S 27 TYR 0.032 0.002 TYR S 178 ARG 0.004 0.000 ARG S 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.987 Fit side-chains REVERT: A 35 LYS cc_start: 0.8564 (mttp) cc_final: 0.8236 (mtmt) REVERT: B 325 MET cc_start: 0.8453 (tpp) cc_final: 0.8207 (tpp) REVERT: C 20 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8273 (mtmm) REVERT: C 47 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7797 (mt-10) REVERT: C 53 PRO cc_start: 0.7155 (Cg_exo) cc_final: 0.6937 (Cg_endo) REVERT: R 33 LYS cc_start: 0.4799 (ptpt) cc_final: 0.4578 (pttm) REVERT: R 115 MET cc_start: 0.7393 (ttp) cc_final: 0.7078 (ttm) REVERT: R 147 ARG cc_start: 0.6376 (ttt-90) cc_final: 0.5990 (ttt180) REVERT: R 157 MET cc_start: 0.6415 (tpp) cc_final: 0.6183 (tpp) REVERT: R 245 LYS cc_start: 0.6932 (mmpt) cc_final: 0.6726 (mmpt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 1.3204 time to fit residues: 222.6937 Evaluate side-chains 131 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.7018 > 50: distance: 75 - 116: 7.550 distance: 78 - 113: 6.360 distance: 97 - 105: 14.315 distance: 105 - 106: 11.841 distance: 106 - 107: 8.224 distance: 106 - 109: 9.576 distance: 107 - 113: 4.232 distance: 108 - 182: 6.542 distance: 109 - 110: 10.695 distance: 110 - 111: 8.230 distance: 110 - 112: 5.967 distance: 113 - 114: 5.453 distance: 114 - 115: 10.734 distance: 114 - 117: 8.611 distance: 115 - 116: 5.309 distance: 115 - 124: 13.225 distance: 117 - 118: 7.998 distance: 118 - 119: 14.153 distance: 118 - 120: 12.323 distance: 119 - 121: 7.722 distance: 120 - 122: 4.922 distance: 121 - 123: 10.173 distance: 122 - 123: 7.703 distance: 124 - 125: 4.062 distance: 125 - 126: 4.414 distance: 125 - 128: 3.740 distance: 126 - 127: 12.668 distance: 126 - 132: 7.236 distance: 128 - 129: 15.220 distance: 129 - 130: 16.161 distance: 129 - 131: 9.346 distance: 132 - 133: 14.569 distance: 133 - 134: 4.927 distance: 133 - 136: 8.975 distance: 134 - 135: 9.200 distance: 134 - 140: 20.263 distance: 136 - 137: 44.513 distance: 137 - 138: 32.630 distance: 137 - 139: 35.649 distance: 140 - 141: 4.933 distance: 141 - 142: 13.844 distance: 141 - 144: 15.687 distance: 142 - 143: 4.915 distance: 142 - 151: 15.556 distance: 144 - 145: 20.744 distance: 145 - 146: 18.855 distance: 146 - 147: 23.128 distance: 147 - 148: 4.322 distance: 148 - 149: 5.028 distance: 148 - 150: 9.137 distance: 151 - 152: 9.687 distance: 152 - 153: 5.529 distance: 152 - 155: 6.433 distance: 153 - 154: 10.721 distance: 153 - 156: 8.028 distance: 156 - 157: 4.275 distance: 157 - 160: 5.652 distance: 158 - 159: 5.687 distance: 158 - 164: 9.233 distance: 160 - 161: 13.516 distance: 161 - 162: 9.283 distance: 161 - 163: 7.801 distance: 164 - 165: 3.515 distance: 165 - 166: 5.351 distance: 165 - 168: 10.969 distance: 166 - 167: 7.641 distance: 166 - 173: 21.963 distance: 168 - 169: 9.097 distance: 169 - 170: 4.053 distance: 170 - 171: 5.999 distance: 170 - 172: 6.611 distance: 173 - 174: 3.212 distance: 174 - 177: 7.172 distance: 175 - 176: 13.830 distance: 175 - 182: 11.643 distance: 177 - 178: 10.145 distance: 178 - 179: 6.915 distance: 179 - 180: 8.150 distance: 179 - 181: 5.120 distance: 182 - 183: 4.615 distance: 183 - 184: 5.924 distance: 183 - 186: 9.239 distance: 184 - 185: 7.379 distance: 184 - 190: 6.772 distance: 186 - 187: 17.179 distance: 187 - 188: 10.527 distance: 187 - 189: 7.497