Starting phenix.real_space_refine on Sat Aug 3 18:29:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1u_23118/08_2024/7l1u_23118.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1u_23118/08_2024/7l1u_23118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1u_23118/08_2024/7l1u_23118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1u_23118/08_2024/7l1u_23118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1u_23118/08_2024/7l1u_23118.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1u_23118/08_2024/7l1u_23118.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 63 5.16 5 C 5586 2.51 5 N 1498 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 310": "OD1" <-> "OD2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 137": "OD1" <-> "OD2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H ASP 223": "OD1" <-> "OD2" Residue "H PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 246": "OE1" <-> "OE2" Residue "R GLU 52": "OE1" <-> "OE2" Residue "R TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 337": "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: 8723 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1802 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2496 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 97 Chain: "C" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 422 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1719 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "R" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2220 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.67, per 1000 atoms: 0.65 Number of scatterers: 8723 At special positions: 0 Unit cell: (112.56, 108.36, 137.76, 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 63 16.00 O 1576 8.00 N 1498 7.00 C 5586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 210 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 2.0 seconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 36.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.291A pdb=" N ARG A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.544A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.870A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.732A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.752A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.184A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.519A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 6 through 24 removed outlier: 3.764A 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 'H' and resid 28 through 32 removed outlier: 3.594A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.572A pdb=" N ASP H 223 " --> pdb=" O GLU H 220 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 220 through 224' Processing helix chain 'R' and resid 52 through 55 Processing helix chain 'R' and resid 56 through 82 Processing helix chain 'R' and resid 89 through 107 removed outlier: 3.947A pdb=" N ILE R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 118 Processing helix chain 'R' and resid 122 through 157 removed outlier: 4.083A pdb=" N LEU R 126 " --> pdb=" O PHE R 122 " (cutoff:3.500A) Proline residue: R 131 - end of helix Processing helix chain 'R' and resid 165 through 184 removed outlier: 3.854A pdb=" N MET R 184 " --> pdb=" O SER R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 190 removed outlier: 4.025A pdb=" N VAL R 190 " --> pdb=" O PRO R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 232 removed outlier: 3.948A pdb=" N MET R 222 " --> pdb=" O ILE R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 250 Processing helix chain 'R' and resid 293 through 316 removed outlier: 4.153A pdb=" N LYS R 301 " --> pdb=" O ARG R 297 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR R 302 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA R 303 " --> pdb=" O ARG R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 328 removed outlier: 3.707A pdb=" N SER R 321 " --> pdb=" O TYR R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 364 removed outlier: 3.805A pdb=" N VAL R 342 " --> pdb=" O ASP R 338 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 376 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.270A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.792A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.017A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.083A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.600A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.508A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.712A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.783A 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 277 removed outlier: 6.444A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.523A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.545A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 194 through 195 removed outlier: 5.529A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 191 through 195 430 hydrogen bonds defined for protein. 1218 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: 2.48 Time building geometry restraints manager: 3.62 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: 2677 1.34 - 1.46: 1900 1.46 - 1.58: 4241 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 8910 Sorted by residual: bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.722 0.086 3.30e-02 9.18e+02 6.85e+00 bond pdb=" CA GLN H 142 " pdb=" CB GLN H 142 " ideal model delta sigma weight residual 1.527 1.462 0.065 2.48e-02 1.63e+03 6.83e+00 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.419 0.079 3.10e-02 1.04e+03 6.52e+00 bond pdb=" C TYR A 360 " pdb=" N PRO A 361 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.11e-02 8.12e+03 6.03e+00 bond pdb=" CG LEU B 79 " pdb=" CD2 LEU B 79 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.45e+00 ... (remaining 8905 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.33: 144 105.33 - 112.53: 4598 112.53 - 119.73: 3090 119.73 - 126.93: 4169 126.93 - 134.13: 113 Bond angle restraints: 12114 Sorted by residual: angle pdb=" C LYS B 301 " pdb=" N ALA B 302 " pdb=" CA ALA B 302 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C PRO B 236 " pdb=" N ASN B 237 " pdb=" CA ASN B 237 " ideal model delta sigma weight residual 122.38 115.79 6.59 1.81e+00 3.05e-01 1.32e+01 angle pdb=" C VAL H 48 " pdb=" N ALA H 49 " pdb=" CA ALA H 49 " ideal model delta sigma weight residual 121.75 115.93 5.82 1.73e+00 3.34e-01 1.13e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N GLY B 282 " pdb=" CA GLY B 282 " pdb=" C GLY B 282 " ideal model delta sigma weight residual 116.01 110.71 5.30 1.64e+00 3.72e-01 1.04e+01 ... (remaining 12109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 4637 15.93 - 31.85: 498 31.85 - 47.78: 93 47.78 - 63.71: 14 63.71 - 79.64: 4 Dihedral angle restraints: 5246 sinusoidal: 1905 harmonic: 3341 Sorted by residual: dihedral pdb=" CA PHE R 121 " pdb=" C PHE R 121 " pdb=" N PHE R 122 " pdb=" CA PHE R 122 " ideal model delta harmonic sigma weight residual 180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA SER H 208 " pdb=" C SER H 208 " pdb=" N GLY H 209 " pdb=" CA GLY H 209 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ALA R 234 " pdb=" C ALA R 234 " pdb=" N PRO R 235 " pdb=" CA PRO R 235 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 5243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 878 0.050 - 0.100: 391 0.100 - 0.150: 113 0.150 - 0.200: 19 0.200 - 0.250: 8 Chirality restraints: 1409 Sorted by residual: chirality pdb=" CB VAL R 73 " pdb=" CA VAL R 73 " pdb=" CG1 VAL R 73 " pdb=" CG2 VAL R 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE H 100 " pdb=" CA ILE H 100 " pdb=" CG1 ILE H 100 " pdb=" CG2 ILE H 100 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL H 48 " pdb=" CA VAL H 48 " pdb=" CG1 VAL H 48 " pdb=" CG2 VAL H 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1406 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA R 234 " 0.050 5.00e-02 4.00e+02 7.49e-02 8.97e+00 pdb=" N PRO R 235 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 235 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 235 " 0.042 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 7.12e-02 8.12e+00 pdb=" N PRO B 236 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.036 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=" C ALA B 193 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO B 194 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.038 5.00e-02 4.00e+02 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1121 2.74 - 3.28: 7690 3.28 - 3.82: 13832 3.82 - 4.36: 15948 4.36 - 4.90: 29381 Nonbonded interactions: 67972 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.202 3.040 nonbonded pdb=" O SER A 250 " pdb=" OG SER A 250 " model vdw 2.288 3.040 nonbonded pdb=" O VAL R 114 " pdb=" OH TYR R 343 " model vdw 2.307 3.040 nonbonded pdb=" OE2 GLU A 15 " pdb=" OH TYR H 175 " model vdw 2.308 3.040 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.315 3.040 ... (remaining 67967 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: 3.800 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.580 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.011 0.086 8910 Z= 0.709 Angle : 0.996 10.490 12114 Z= 0.570 Chirality : 0.062 0.250 1409 Planarity : 0.007 0.075 1518 Dihedral : 13.515 79.637 3077 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.78 % Allowed : 9.22 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -3.21 (0.20), residues: 1128 helix: -2.10 (0.20), residues: 391 sheet: -1.25 (0.28), residues: 294 loop : -2.62 (0.23), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 47 HIS 0.008 0.002 HIS B 142 PHE 0.031 0.003 PHE B 199 TYR 0.037 0.003 TYR B 59 ARG 0.007 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 1.006 Fit side-chains REVERT: A 209 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8067 (mt-10) REVERT: B 293 ASN cc_start: 0.8425 (p0) cc_final: 0.8137 (p0) REVERT: C 47 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7554 (mp0) REVERT: H 87 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.7995 (mtt-85) REVERT: R 122 PHE cc_start: 0.6672 (m-80) cc_final: 0.6379 (m-80) REVERT: R 191 MET cc_start: 0.8699 (mmt) cc_final: 0.8118 (mmp) REVERT: R 239 MET cc_start: 0.8077 (ttm) cc_final: 0.7823 (mtp) REVERT: R 339 ARG cc_start: 0.7272 (ptm-80) cc_final: 0.6497 (ttt-90) outliers start: 7 outliers final: 5 residues processed: 155 average time/residue: 0.2547 time to fit residues: 51.6182 Evaluate side-chains 130 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 87 THR 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: 56.4979 > 50: distance: 21 - 37: 3.008 distance: 23 - 43: 4.076 distance: 29 - 54: 18.194 distance: 36 - 65: 18.077 distance: 40 - 73: 11.314 distance: 43 - 44: 5.337 distance: 44 - 45: 7.288 distance: 44 - 47: 6.824 distance: 45 - 46: 4.010 distance: 45 - 54: 13.064 distance: 46 - 80: 20.355 distance: 48 - 49: 6.435 distance: 48 - 50: 8.660 distance: 49 - 51: 8.192 distance: 50 - 52: 10.263 distance: 51 - 53: 8.576 distance: 52 - 53: 6.797 distance: 54 - 55: 11.415 distance: 55 - 56: 12.572 distance: 55 - 58: 4.787 distance: 56 - 57: 4.463 distance: 56 - 65: 8.709 distance: 57 - 87: 24.877 distance: 59 - 60: 5.762 distance: 59 - 61: 12.297 distance: 60 - 62: 15.313 distance: 61 - 63: 6.815 distance: 62 - 64: 14.043 distance: 63 - 64: 8.223 distance: 65 - 66: 13.175 distance: 66 - 67: 17.524 distance: 66 - 69: 4.514 distance: 67 - 68: 29.431 distance: 67 - 73: 19.969 distance: 69 - 70: 8.373 distance: 70 - 71: 5.929 distance: 70 - 72: 8.386 distance: 73 - 74: 28.830 distance: 74 - 75: 21.391 distance: 74 - 77: 24.488 distance: 75 - 76: 42.269 distance: 75 - 80: 24.138 distance: 77 - 78: 7.222 distance: 77 - 79: 26.381 distance: 80 - 81: 7.467 distance: 81 - 82: 27.652 distance: 81 - 84: 16.874 distance: 82 - 83: 9.111 distance: 82 - 87: 19.586 distance: 84 - 85: 24.326 distance: 84 - 86: 8.833 distance: 87 - 88: 17.547 distance: 88 - 89: 13.366 distance: 88 - 91: 8.596 distance: 89 - 90: 5.064 distance: 89 - 99: 5.287 distance: 90 - 119: 8.449 distance: 91 - 92: 8.526 distance: 92 - 93: 13.607 distance: 92 - 94: 6.280 distance: 93 - 95: 17.049 distance: 94 - 96: 8.882 distance: 95 - 97: 7.284 distance: 96 - 97: 9.480 distance: 97 - 98: 11.795 distance: 99 - 100: 4.594 distance: 100 - 101: 3.093 distance: 100 - 103: 13.324 distance: 101 - 102: 4.515 distance: 101 - 107: 10.274 distance: 102 - 127: 9.397 distance: 103 - 104: 6.227 distance: 104 - 105: 5.385 distance: 105 - 106: 10.512 distance: 107 - 108: 8.009 distance: 108 - 109: 6.073 distance: 108 - 111: 11.262 distance: 109 - 110: 6.940 distance: 109 - 112: 6.005 distance: 110 - 133: 7.959 distance: 112 - 113: 9.344 distance: 112 - 118: 9.876 distance: 113 - 114: 3.318 distance: 113 - 116: 15.554 distance: 114 - 115: 11.363 distance: 114 - 119: 11.833 distance: 115 - 138: 5.668 distance: 116 - 117: 6.293 distance: 117 - 118: 8.803 distance: 119 - 120: 8.187 distance: 120 - 121: 4.175 distance: 120 - 123: 6.438 distance: 121 - 122: 6.422 distance: 121 - 127: 5.163 distance: 122 - 146: 9.081 distance: 123 - 124: 13.883 distance: 124 - 125: 11.422 distance: 124 - 126: 9.709 distance: 130 - 152: 3.014