Starting phenix.real_space_refine on Sat Aug 3 17:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1f_33562/08_2024/7y1f_33562.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1f_33562/08_2024/7y1f_33562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1f_33562/08_2024/7y1f_33562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1f_33562/08_2024/7y1f_33562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1f_33562/08_2024/7y1f_33562.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1f_33562/08_2024/7y1f_33562.cif" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5561 2.51 5 N 1480 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 7": "NH1" <-> "NH2" Residue "R TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 188": "NH1" <-> "NH2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 272": "NH1" <-> "NH2" Residue "R ASP 325": "OD1" <-> "OD2" Residue "R PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 359": "NH1" <-> "NH2" Residue "R ASP 368": "OD1" <-> "OD2" Residue "R ARG 369": "NH1" <-> "NH2" Residue "R PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 436": "OD1" <-> "OD2" Residue "R PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 441": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E ASP 211": "OD1" <-> "OD2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8691 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 80 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "R" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2256 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 4.69, per 1000 atoms: 0.54 Number of scatterers: 8691 At special positions: 0 Unit cell: (102.6, 112.32, 135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1590 8.00 N 1480 7.00 C 5561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 233 " - pdb=" SG CYS R 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 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: 2.95 Conformation dependent library (CDL) restraints added in 1.4 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 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: 25 helices and 14 sheets defined 35.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.238A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.575A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.208A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.571A pdb=" N SER A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.979A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.971A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 345 Processing helix chain 'R' and resid 159 through 189 Processing helix chain 'R' and resid 194 through 212 removed outlier: 3.768A pdb=" N ILE R 198 " --> pdb=" O THR R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 223 removed outlier: 4.097A pdb=" N VAL R 220 " --> pdb=" O PHE R 216 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR R 221 " --> pdb=" O GLN R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 264 removed outlier: 3.568A pdb=" N HIS R 264 " --> pdb=" O ILE R 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 272 removed outlier: 4.019A pdb=" N LEU R 269 " --> pdb=" O PRO R 265 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP R 270 " --> pdb=" O VAL R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 298 removed outlier: 4.137A pdb=" N VAL R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 337 Processing helix chain 'R' and resid 337 through 357 removed outlier: 4.213A pdb=" N SER R 357 " --> pdb=" O LEU R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 399 removed outlier: 3.782A pdb=" N ASP R 368 " --> pdb=" O SER R 364 " (cutoff:3.500A) Proline residue: R 391 - end of helix Processing helix chain 'R' and resid 409 through 433 removed outlier: 4.344A pdb=" N SER R 413 " --> pdb=" O ALA R 409 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER R 425 " --> pdb=" O GLY R 421 " (cutoff:3.500A) Proline residue: R 429 - end of helix Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.965A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.859A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.615A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.519A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.545A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.392A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 226 removed outlier: 5.654A pdb=" N PHE A 223 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL A 225 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 299 through 302 removed outlier: 3.794A pdb=" N GLY R 300 " --> pdb=" O SER R 313 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER R 313 " --> pdb=" O GLY R 300 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU R 311 " --> pdb=" O LYS R 302 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.659A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.696A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.167A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.470A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.690A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.700A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.777A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.137A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1131 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: 2.42 Time building geometry restraints manager: 3.28 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: 2767 1.34 - 1.47: 2247 1.47 - 1.59: 3770 1.59 - 1.72: 0 1.72 - 1.84: 87 Bond restraints: 8871 Sorted by residual: bond pdb=" C GLU E 222 " pdb=" N TYR E 223 " ideal model delta sigma weight residual 1.335 1.247 0.087 3.04e-02 1.08e+03 8.23e+00 bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.414 0.099 3.90e-02 6.57e+02 6.49e+00 bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.731 0.077 3.30e-02 9.18e+02 5.45e+00 bond pdb=" CG1 ILE B 338 " pdb=" CD1 ILE B 338 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.29e+00 bond pdb=" CB VAL B 112 " pdb=" CG1 VAL B 112 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.16e+00 ... (remaining 8866 not shown) Histogram of bond angle deviations from ideal: 97.62 - 104.95: 126 104.95 - 112.27: 4398 112.27 - 119.60: 2954 119.60 - 126.93: 4430 126.93 - 134.25: 127 Bond angle restraints: 12035 Sorted by residual: angle pdb=" C GLU R 305 " pdb=" N ASP R 306 " pdb=" CA ASP R 306 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.26e+01 angle pdb=" CA LEU A 353 " pdb=" CB LEU A 353 " pdb=" CG LEU A 353 " ideal model delta sigma weight residual 116.30 133.18 -16.88 3.50e+00 8.16e-02 2.33e+01 angle pdb=" C ALA E 209 " pdb=" N GLU E 210 " pdb=" CA GLU E 210 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C ASP B 247 " pdb=" N ALA B 248 " pdb=" CA ALA B 248 " ideal model delta sigma weight residual 122.74 128.70 -5.96 1.44e+00 4.82e-01 1.71e+01 angle pdb=" C ASP B 246 " pdb=" N ASP B 247 " pdb=" CA ASP B 247 " ideal model delta sigma weight residual 120.60 127.21 -6.61 1.60e+00 3.91e-01 1.71e+01 ... (remaining 12030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4701 17.11 - 34.23: 435 34.23 - 51.34: 93 51.34 - 68.45: 8 68.45 - 85.57: 10 Dihedral angle restraints: 5247 sinusoidal: 1964 harmonic: 3283 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 170.63 -77.63 1 1.00e+01 1.00e-02 7.54e+01 dihedral pdb=" CA LYS A 10 " pdb=" C LYS A 10 " pdb=" N ALA A 11 " pdb=" CA ALA A 11 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA LYS A 349 " pdb=" C LYS A 349 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 5244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1214 0.084 - 0.169: 164 0.169 - 0.253: 16 0.253 - 0.338: 2 0.338 - 0.422: 2 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB ILE B 338 " pdb=" CA ILE B 338 " pdb=" CG1 ILE B 338 " pdb=" CG2 ILE B 338 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1395 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " -0.032 2.00e-02 2.50e+03 2.61e-02 1.70e+01 pdb=" CG TRP B 332 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET R 214 " 0.066 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO R 215 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO R 215 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO R 215 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.021 2.00e-02 2.50e+03 1.90e-02 7.22e+00 pdb=" CG TYR B 105 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " -0.001 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1297 2.75 - 3.29: 8569 3.29 - 3.83: 14672 3.83 - 4.36: 17392 4.36 - 4.90: 30149 Nonbonded interactions: 72079 Sorted by model distance: nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.215 3.040 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.234 3.040 nonbonded pdb=" O ALA R 419 " pdb=" OG1 THR R 423 " model vdw 2.241 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.242 3.040 nonbonded pdb=" O VAL R 386 " pdb=" OG1 THR R 390 " model vdw 2.250 3.040 ... (remaining 72074 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: 0.720 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.760 Find NCS groups from input model: 0.080 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 0.099 8871 Z= 0.463 Angle : 1.118 16.879 12035 Z= 0.604 Chirality : 0.060 0.422 1398 Planarity : 0.007 0.098 1505 Dihedral : 13.790 85.567 3117 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.25 (0.23), residues: 1113 helix: -1.02 (0.24), residues: 357 sheet: -1.36 (0.33), residues: 251 loop : -1.81 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP B 332 HIS 0.013 0.003 HIS B 183 PHE 0.034 0.003 PHE A 323 TYR 0.047 0.003 TYR B 105 ARG 0.028 0.002 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 0.923 Fit side-chains REVERT: A 303 ILE cc_start: 0.7538 (mt) cc_final: 0.7302 (mm) REVERT: A 333 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7379 (tp40) REVERT: A 337 ASP cc_start: 0.7943 (m-30) cc_final: 0.7657 (m-30) REVERT: R 214 MET cc_start: 0.6920 (ttm) cc_final: 0.6566 (ttp) REVERT: R 221 TYR cc_start: 0.7337 (t80) cc_final: 0.6873 (t80) REVERT: R 222 LEU cc_start: 0.6161 (mm) cc_final: 0.5681 (mm) REVERT: B 43 ILE cc_start: 0.8389 (mt) cc_final: 0.8066 (mt) REVERT: E 223 TYR cc_start: 0.7885 (m-80) cc_final: 0.7077 (m-80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2064 time to fit residues: 65.6264 Evaluate side-chains 197 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.0670 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.0050 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 322 HIS ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 266 HIS E 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8871 Z= 0.184 Angle : 0.656 9.753 12035 Z= 0.345 Chirality : 0.044 0.233 1398 Planarity : 0.005 0.065 1505 Dihedral : 5.589 24.183 1224 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.73 % Allowed : 8.97 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.15 (0.24), residues: 1113 helix: 0.61 (0.26), residues: 334 sheet: -1.10 (0.33), residues: 250 loop : -1.46 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 332 HIS 0.004 0.001 HIS A 188 PHE 0.032 0.002 PHE R 439 TYR 0.019 0.001 TYR R 242 ARG 0.006 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 221 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 258 TRP cc_start: 0.5122 (m100) cc_final: 0.3020 (p-90) REVERT: A 333 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7315 (tp40) REVERT: A 337 ASP cc_start: 0.7839 (m-30) cc_final: 0.7626 (m-30) REVERT: R 187 ILE cc_start: 0.6978 (mm) cc_final: 0.6650 (mt) REVERT: R 214 MET cc_start: 0.6779 (ttm) cc_final: 0.6436 (ttm) REVERT: R 223 MET cc_start: 0.7251 (tmm) cc_final: 0.7033 (ppp) REVERT: R 315 GLN cc_start: 0.5632 (mp10) cc_final: 0.5034 (mp10) REVERT: R 351 MET cc_start: 0.7838 (ttt) cc_final: 0.7622 (ttt) REVERT: B 79 LEU cc_start: 0.8391 (mt) cc_final: 0.8063 (mt) REVERT: B 111 TYR cc_start: 0.7820 (m-80) cc_final: 0.7603 (m-80) REVERT: E 34 MET cc_start: 0.6304 (mmp) cc_final: 0.6100 (mmp) REVERT: E 47 TRP cc_start: 0.6836 (t60) cc_final: 0.6437 (t60) REVERT: E 206 ARG cc_start: 0.7937 (tpp-160) cc_final: 0.7679 (tpp-160) outliers start: 16 outliers final: 13 residues processed: 225 average time/residue: 0.2127 time to fit residues: 64.7185 Evaluate side-chains 204 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8871 Z= 0.356 Angle : 0.732 8.608 12035 Z= 0.385 Chirality : 0.047 0.394 1398 Planarity : 0.005 0.057 1505 Dihedral : 5.831 28.922 1224 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.35 % Allowed : 12.32 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.11 (0.24), residues: 1113 helix: 0.61 (0.26), residues: 345 sheet: -1.13 (0.32), residues: 257 loop : -1.43 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.006 0.002 HIS A 213 PHE 0.021 0.002 PHE R 439 TYR 0.023 0.002 TYR B 105 ARG 0.007 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 214 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7616 (mmp) cc_final: 0.6614 (mmp) REVERT: A 333 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7634 (tp40) REVERT: A 337 ASP cc_start: 0.7978 (m-30) cc_final: 0.7641 (m-30) REVERT: R 187 ILE cc_start: 0.7019 (mm) cc_final: 0.6682 (mt) REVERT: R 214 MET cc_start: 0.7235 (ttm) cc_final: 0.6728 (ttm) REVERT: R 223 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6919 (ppp) REVERT: R 354 ARG cc_start: 0.7494 (tpp80) cc_final: 0.6092 (tpt90) REVERT: B 256 ARG cc_start: 0.7480 (mtp85) cc_final: 0.7147 (ttm110) REVERT: E 47 TRP cc_start: 0.7017 (t60) cc_final: 0.6728 (t60) REVERT: E 93 MET cc_start: 0.6237 (tmm) cc_final: 0.5924 (ptm) REVERT: E 160 THR cc_start: 0.7607 (OUTLIER) cc_final: 0.7377 (m) outliers start: 31 outliers final: 23 residues processed: 230 average time/residue: 0.2092 time to fit residues: 65.2845 Evaluate side-chains 224 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 51 optimal weight: 7.9990 chunk 11 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8871 Z= 0.189 Angle : 0.640 8.918 12035 Z= 0.332 Chirality : 0.043 0.209 1398 Planarity : 0.004 0.049 1505 Dihedral : 5.279 23.327 1224 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.38 % Allowed : 16.22 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.24), residues: 1113 helix: 1.05 (0.26), residues: 339 sheet: -0.90 (0.33), residues: 246 loop : -1.28 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 332 HIS 0.002 0.001 HIS A 188 PHE 0.035 0.002 PHE A 323 TYR 0.016 0.001 TYR R 242 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 218 time to evaluate : 0.938 Fit side-chains REVERT: A 247 MET cc_start: 0.7609 (mmp) cc_final: 0.7017 (mmp) REVERT: A 333 GLN cc_start: 0.7817 (mm110) cc_final: 0.7482 (tp40) REVERT: A 337 ASP cc_start: 0.7911 (m-30) cc_final: 0.7433 (m-30) REVERT: R 187 ILE cc_start: 0.6814 (mm) cc_final: 0.6473 (mt) REVERT: R 214 MET cc_start: 0.7285 (ttm) cc_final: 0.6889 (ttm) REVERT: R 223 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6800 (ppp) REVERT: R 354 ARG cc_start: 0.7599 (tpp80) cc_final: 0.6247 (tpt90) REVERT: B 82 TRP cc_start: 0.7224 (m100) cc_final: 0.6623 (m100) REVERT: B 156 GLN cc_start: 0.7354 (mt0) cc_final: 0.7146 (mt0) REVERT: E 47 TRP cc_start: 0.6761 (t60) cc_final: 0.6361 (t60) REVERT: E 93 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.6062 (ptm) REVERT: E 160 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7184 (p) outliers start: 22 outliers final: 17 residues processed: 224 average time/residue: 0.2146 time to fit residues: 64.9416 Evaluate side-chains 220 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8871 Z= 0.222 Angle : 0.647 8.813 12035 Z= 0.335 Chirality : 0.044 0.248 1398 Planarity : 0.004 0.047 1505 Dihedral : 5.230 25.207 1224 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.78 % Allowed : 16.76 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1113 helix: 1.24 (0.26), residues: 338 sheet: -0.93 (0.32), residues: 258 loop : -1.15 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.004 0.001 HIS B 225 PHE 0.033 0.002 PHE R 439 TYR 0.016 0.001 TYR R 242 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 221 time to evaluate : 0.977 Fit side-chains REVERT: A 247 MET cc_start: 0.7639 (mmp) cc_final: 0.7225 (mmp) REVERT: A 337 ASP cc_start: 0.7801 (m-30) cc_final: 0.7216 (m-30) REVERT: A 341 ASP cc_start: 0.7643 (m-30) cc_final: 0.7335 (m-30) REVERT: R 187 ILE cc_start: 0.6784 (mm) cc_final: 0.6432 (mt) REVERT: R 214 MET cc_start: 0.7357 (ttm) cc_final: 0.6992 (ttm) REVERT: R 223 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6873 (ppp) REVERT: R 354 ARG cc_start: 0.7474 (tpp80) cc_final: 0.6164 (tpt90) REVERT: R 377 LEU cc_start: 0.7017 (tp) cc_final: 0.6769 (tt) REVERT: R 412 SER cc_start: 0.7379 (m) cc_final: 0.7169 (m) REVERT: B 82 TRP cc_start: 0.7163 (m100) cc_final: 0.6594 (m100) REVERT: B 156 GLN cc_start: 0.7308 (mt0) cc_final: 0.7096 (mt0) REVERT: B 183 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.6966 (m170) REVERT: C 21 MET cc_start: 0.4256 (tmm) cc_final: 0.3615 (tmm) REVERT: E 6 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.5150 (pt0) REVERT: E 47 TRP cc_start: 0.6785 (t60) cc_final: 0.6321 (t60) REVERT: E 93 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.6119 (ptm) REVERT: E 160 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.7125 (p) outliers start: 35 outliers final: 24 residues processed: 234 average time/residue: 0.2071 time to fit residues: 66.7724 Evaluate side-chains 232 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 52.8767 > 50: distance: 27 - 47: 4.494 distance: 41 - 42: 3.929 distance: 42 - 43: 5.784 distance: 42 - 47: 4.401 distance: 44 - 46: 4.713 distance: 47 - 48: 6.103 distance: 48 - 49: 8.614 distance: 48 - 51: 5.082 distance: 49 - 50: 6.327 distance: 49 - 55: 3.688 distance: 51 - 52: 4.197 distance: 52 - 53: 7.090 distance: 52 - 54: 7.812 distance: 55 - 56: 23.805 distance: 56 - 57: 36.511 distance: 57 - 58: 20.553 distance: 57 - 59: 27.624 distance: 59 - 60: 12.726 distance: 60 - 61: 18.761 distance: 61 - 62: 37.919 distance: 61 - 63: 23.293 distance: 63 - 64: 15.427 distance: 64 - 65: 13.906 distance: 64 - 67: 21.836 distance: 65 - 66: 8.809 distance: 65 - 70: 12.132 distance: 67 - 68: 31.463 distance: 67 - 69: 23.668 distance: 70 - 71: 13.113 distance: 70 - 142: 20.801 distance: 71 - 72: 13.922 distance: 71 - 74: 13.720 distance: 72 - 73: 6.526 distance: 72 - 79: 5.909 distance: 74 - 75: 7.889 distance: 75 - 76: 13.488 distance: 76 - 77: 8.612 distance: 77 - 78: 17.459 distance: 79 - 80: 12.489 distance: 80 - 81: 11.163 distance: 80 - 83: 15.913 distance: 81 - 82: 15.197 distance: 81 - 86: 4.945 distance: 83 - 84: 22.741 distance: 83 - 85: 10.752 distance: 86 - 87: 11.505 distance: 87 - 88: 11.396 distance: 87 - 90: 7.917 distance: 88 - 89: 18.585 distance: 88 - 97: 12.443 distance: 90 - 91: 6.971 distance: 91 - 92: 9.015 distance: 92 - 93: 3.865 distance: 93 - 94: 4.689 distance: 94 - 95: 4.896 distance: 94 - 96: 4.915 distance: 97 - 98: 18.681 distance: 98 - 99: 14.706 distance: 98 - 101: 7.948 distance: 99 - 100: 3.628 distance: 99 - 106: 3.378 distance: 102 - 103: 18.940 distance: 103 - 104: 24.197 distance: 103 - 105: 25.079 distance: 107 - 108: 17.746 distance: 107 - 110: 13.355 distance: 108 - 109: 24.621 distance: 108 - 114: 20.950 distance: 110 - 111: 5.557 distance: 111 - 112: 14.459 distance: 111 - 113: 21.643