Starting phenix.real_space_refine on Sun Mar 17 14:46:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xis_22199/03_2024/6xis_22199.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xis_22199/03_2024/6xis_22199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xis_22199/03_2024/6xis_22199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xis_22199/03_2024/6xis_22199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xis_22199/03_2024/6xis_22199.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xis_22199/03_2024/6xis_22199.pdb" } resolution = 3.9 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= 0.002 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8723 atoms to isotropic. 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 52 5.16 5 C 6086 2.51 5 N 1548 2.21 5 O 1750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 217": "OD1" <-> "OD2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 217": "OD1" <-> "OD2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9436 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2357 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 300} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2361 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 9, 'TRANS': 300} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2357 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 9, 'TRANS': 300} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2361 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 9, 'TRANS': 300} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 5.41, per 1000 atoms: 0.57 Number of scatterers: 9436 At special positions: 0 Unit cell: (90.3, 90.3, 138.03, 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 52 16.00 O 1750 8.00 N 1548 7.00 C 6086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 166 " distance=1.57 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 166 " distance=2.07 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 166 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.8 seconds 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 23 sheets defined 32.1% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.799A pdb=" N ASP A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 117 Processing helix chain 'A' and resid 119 through 128 removed outlier: 4.552A pdb=" N MET A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N HIS A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 removed outlier: 3.891A pdb=" N SER A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 196 removed outlier: 4.090A pdb=" N LEU A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 Processing helix chain 'B' and resid 80 through 87 removed outlier: 3.584A pdb=" N VAL B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 117 removed outlier: 3.652A pdb=" N TYR B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 170 through 196 Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'C' and resid 78 through 88 removed outlier: 3.508A pdb=" N ILE C 82 " --> pdb=" O TYR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 117 removed outlier: 3.549A pdb=" N TYR C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 116 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA C 117 " --> pdb=" O TRP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 4.383A pdb=" N ASP C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.643A pdb=" N TRP C 131 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 removed outlier: 3.784A pdb=" N SER C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 196 removed outlier: 3.890A pdb=" N LEU C 174 " --> pdb=" O ILE C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.953A pdb=" N LYS C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 332 Processing helix chain 'C' and resid 353 through 358 removed outlier: 4.214A pdb=" N HIS C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 358' Processing helix chain 'C' and resid 368 through 381 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.512A pdb=" N THR D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 117 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 170 through 196 removed outlier: 3.871A pdb=" N LEU D 174 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 332 removed outlier: 3.522A pdb=" N ILE D 332 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 207 Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 207 Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 262 removed outlier: 4.571A pdb=" N ALA A 241 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL A 235 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 275 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 262 removed outlier: 4.571A pdb=" N ALA A 241 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA A 237 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU A 311 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A 239 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 309 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA A 241 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A 307 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU A 243 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU A 305 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 345 Processing sheet with id=AA7, first strand: chain 'B' and resid 205 through 207 Processing sheet with id=AA8, first strand: chain 'B' and resid 205 through 207 Processing sheet with id=AA9, first strand: chain 'B' and resid 254 through 262 removed outlier: 5.326A pdb=" N LYS B 247 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA B 241 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 312 " --> pdb=" O CYS B 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 336 through 338 Processing sheet with id=AB2, first strand: chain 'B' and resid 342 through 345 Processing sheet with id=AB3, first strand: chain 'C' and resid 205 through 207 Processing sheet with id=AB4, first strand: chain 'C' and resid 205 through 207 Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 262 removed outlier: 5.346A pdb=" N LYS C 247 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C 241 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL C 235 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU C 275 " --> pdb=" O VAL C 235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 254 through 262 removed outlier: 5.346A pdb=" N LYS C 247 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C 241 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU C 236 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET C 313 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 336 through 338 Processing sheet with id=AB8, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AB9, first strand: chain 'D' and resid 205 through 207 Processing sheet with id=AC1, first strand: chain 'D' and resid 205 through 207 Processing sheet with id=AC2, first strand: chain 'D' and resid 258 through 262 removed outlier: 4.554A pdb=" N ALA D 241 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 273 " --> pdb=" O ALA D 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 258 through 262 removed outlier: 4.554A pdb=" N ALA D 241 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA D 237 " --> pdb=" O GLU D 311 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU D 311 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE D 239 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE D 309 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA D 241 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL D 307 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU D 243 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU D 305 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 336 through 338 Processing sheet with id=AC5, first strand: chain 'D' and resid 342 through 345 441 hydrogen bonds defined for protein. 1236 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: 2.09 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1533 1.31 - 1.43: 2613 1.43 - 1.56: 5405 1.56 - 1.69: 0 1.69 - 1.82: 80 Bond restraints: 9631 Sorted by residual: bond pdb=" C GLY D 110 " pdb=" N MET D 111 " ideal model delta sigma weight residual 1.334 1.239 0.095 1.27e-02 6.20e+03 5.61e+01 bond pdb=" C MET D 111 " pdb=" N ILE D 112 " ideal model delta sigma weight residual 1.335 1.426 -0.091 1.26e-02 6.30e+03 5.18e+01 bond pdb=" C PRO D 365 " pdb=" O PRO D 365 " ideal model delta sigma weight residual 1.233 1.177 0.056 1.12e-02 7.97e+03 2.51e+01 bond pdb=" N ILE C 255 " pdb=" CA ILE C 255 " ideal model delta sigma weight residual 1.460 1.492 -0.031 7.60e-03 1.73e+04 1.71e+01 bond pdb=" N ASP D 122 " pdb=" CA ASP D 122 " ideal model delta sigma weight residual 1.458 1.494 -0.035 9.00e-03 1.23e+04 1.55e+01 ... (remaining 9626 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.90: 251 106.90 - 113.79: 5372 113.79 - 120.68: 4116 120.68 - 127.57: 3294 127.57 - 134.46: 86 Bond angle restraints: 13119 Sorted by residual: angle pdb=" N PRO C 133 " pdb=" CA PRO C 133 " pdb=" CB PRO C 133 " ideal model delta sigma weight residual 103.25 111.55 -8.30 1.05e+00 9.07e-01 6.25e+01 angle pdb=" N PRO D 133 " pdb=" CA PRO D 133 " pdb=" CB PRO D 133 " ideal model delta sigma weight residual 103.25 111.17 -7.92 1.05e+00 9.07e-01 5.69e+01 angle pdb=" N PRO B 133 " pdb=" CA PRO B 133 " pdb=" CB PRO B 133 " ideal model delta sigma weight residual 103.25 110.84 -7.59 1.05e+00 9.07e-01 5.22e+01 angle pdb=" N PRO A 133 " pdb=" CA PRO A 133 " pdb=" CB PRO A 133 " ideal model delta sigma weight residual 103.25 110.60 -7.35 1.05e+00 9.07e-01 4.90e+01 angle pdb=" N TYR D 159 " pdb=" CA TYR D 159 " pdb=" C TYR D 159 " ideal model delta sigma weight residual 111.28 103.74 7.54 1.09e+00 8.42e-01 4.79e+01 ... (remaining 13114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 5041 16.18 - 32.36: 459 32.36 - 48.54: 109 48.54 - 64.72: 20 64.72 - 80.90: 12 Dihedral angle restraints: 5641 sinusoidal: 2029 harmonic: 3612 Sorted by residual: dihedral pdb=" CB CYS D 134 " pdb=" SG CYS D 134 " pdb=" SG CYS D 166 " pdb=" CB CYS D 166 " ideal model delta sinusoidal sigma weight residual 93.00 170.68 -77.68 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CB CYS A 134 " pdb=" SG CYS A 134 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -154.27 68.27 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS C 134 " pdb=" SG CYS C 134 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 28.47 64.53 1 1.00e+01 1.00e-02 5.47e+01 ... (remaining 5638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 894 0.053 - 0.106: 344 0.106 - 0.160: 210 0.160 - 0.213: 83 0.213 - 0.266: 26 Chirality restraints: 1557 Sorted by residual: chirality pdb=" CA ILE C 255 " pdb=" N ILE C 255 " pdb=" C ILE C 255 " pdb=" CB ILE C 255 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA VAL D 276 " pdb=" N VAL D 276 " pdb=" C VAL D 276 " pdb=" CB VAL D 276 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA CYS A 134 " pdb=" N CYS A 134 " pdb=" C CYS A 134 " pdb=" CB CYS A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1554 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 263 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C ASN C 263 " -0.065 2.00e-02 2.50e+03 pdb=" O ASN C 263 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL C 264 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 263 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ASN D 263 " -0.059 2.00e-02 2.50e+03 pdb=" O ASN D 263 " 0.022 2.00e-02 2.50e+03 pdb=" N VAL D 264 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 165 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS D 165 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS D 165 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS D 166 " -0.020 2.00e-02 2.50e+03 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1198 2.76 - 3.30: 9919 3.30 - 3.83: 15257 3.83 - 4.37: 18172 4.37 - 4.90: 29637 Nonbonded interactions: 74183 Sorted by model distance: nonbonded pdb=" OD1 ASN B 377 " pdb=" N ARG B 378 " model vdw 2.225 2.520 nonbonded pdb=" N GLN A 288 " pdb=" OE1 GLN A 288 " model vdw 2.242 2.520 nonbonded pdb=" SG CYS A 221 " pdb=" OG SER A 282 " model vdw 2.259 2.800 nonbonded pdb=" O LEU A 299 " pdb=" OG1 THR A 329 " model vdw 2.259 2.440 nonbonded pdb=" NH2 ARG A 337 " pdb=" OE1 GLU B 251 " model vdw 2.281 2.520 ... (remaining 74178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 55 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 77 or (resid 78 and (name N or nam \ e CA or name C or name O or name CB )) or resid 79 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 104 or ( \ resid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 \ through 111 or (resid 112 and (name N or name CA or name C or name O or name CB \ )) or resid 113 through 124 or (resid 125 through 128 and (name N or name CA or \ name C or name O or name CB )) or resid 129 through 150 or (resid 151 through 15 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 153 through \ 162 or (resid 163 and (name N or name CA or name C or name O or name CB )) or re \ sid 164 through 274 or (resid 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 314 or (resid 315 through 316 and (name N or nam \ e CA or name C or name O or name CB )) or resid 317 through 348 or (resid 349 an \ d (name N or name CA or name C or name O or name CB )) or resid 350 through 381) \ ) selection = (chain 'B' and (resid 55 through 77 or (resid 78 and (name N or name CA or name \ C or name O or name CB )) or resid 79 through 104 or (resid 105 and (name N or n \ ame CA or name C or name O or name CB )) or resid 106 through 124 or (resid 125 \ through 128 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 9 through 150 or (resid 151 through 152 and (name N or name CA or name C or name \ O or name CB )) or resid 153 through 162 or (resid 163 and (name N or name CA o \ r name C or name O or name CB )) or resid 164 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 173 through 175 or (re \ sid 176 and (name N or name CA or name C or name O or name CB )) or resid 177 th \ rough 224 or (resid 225 and (name N or name CA or name C or name O or name CB )) \ or resid 226 through 274 or (resid 275 and (name N or name CA or name C or name \ O or name CB )) or resid 276 through 348 or (resid 349 and (name N or name CA o \ r name C or name O or name CB )) or resid 350 through 369 or (resid 370 and (nam \ e N or name CA or name C or name O or name CB )) or resid 371 through 381)) selection = (chain 'C' and (resid 55 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 111 or (resid 112 and \ (name N or name CA or name C or name O or name CB )) or resid 113 through 124 o \ r (resid 125 through 128 and (name N or name CA or name C or name O or name CB ) \ ) or resid 129 through 150 or (resid 151 through 152 and (name N or name CA or n \ ame C or name O or name CB )) or resid 153 through 154 or (resid 155 and (name N \ or name CA or name C or name O or name CB )) or resid 156 through 162 or (resid \ 163 and (name N or name CA or name C or name O or name CB )) or resid 164 throu \ gh 171 or (resid 172 and (name N or name CA or name C or name O or name CB )) or \ resid 173 through 175 or (resid 176 and (name N or name CA or name C or name O \ or name CB )) or resid 177 through 224 or (resid 225 and (name N or name CA or n \ ame C or name O or name CB )) or resid 226 through 274 or (resid 275 and (name N \ or name CA or name C or name O or name CB )) or resid 276 through 381)) selection = (chain 'D' and (resid 55 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 77 or (resid 78 and (name N or nam \ e CA or name C or name O or name CB )) or resid 79 through 86 or (resid 87 and ( \ name N or name CA or name C or name O or name CB )) or resid 88 through 104 or ( \ resid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 \ through 111 or (resid 112 and (name N or name CA or name C or name O or name CB \ )) or resid 113 through 151 or (resid 152 and (name N or name CA or name C or na \ me O or name CB )) or resid 153 through 154 or (resid 155 and (name N or name CA \ or name C or name O or name CB )) or resid 156 through 171 or (resid 172 and (n \ ame N or name CA or name C or name O or name CB )) or resid 173 through 175 or ( \ resid 176 and (name N or name CA or name C or name O or name CB )) or resid 177 \ through 224 or (resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 314 or (resid 315 through 316 and (name N or name CA or \ name C or name O or name CB )) or resid 317 through 369 or (resid 370 and (name \ N or name CA or name C or name O or name CB )) or resid 371 through 381)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 4.190 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.890 Find NCS groups from input model: 0.610 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:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 9631 Z= 0.577 Angle : 1.329 9.710 13119 Z= 1.041 Chirality : 0.082 0.266 1557 Planarity : 0.007 0.038 1640 Dihedral : 13.731 80.902 3293 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.33 % Allowed : 1.81 % Favored : 97.86 % Rotamer: Outliers : 3.19 % Allowed : 10.50 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1216 helix: 2.62 (0.25), residues: 340 sheet: 0.88 (0.33), residues: 237 loop : -1.29 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 114 HIS 0.004 0.001 HIS C 357 PHE 0.021 0.002 PHE D 147 TYR 0.017 0.002 TYR C 157 ARG 0.004 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 327 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.7963 (mmtp) cc_final: 0.7660 (mtpp) REVERT: A 322 GLN cc_start: 0.7028 (tt0) cc_final: 0.6822 (mp10) REVERT: A 356 PHE cc_start: 0.8614 (t80) cc_final: 0.8318 (t80) REVERT: A 363 SER cc_start: 0.5594 (t) cc_final: 0.5090 (t) REVERT: B 289 SER cc_start: 0.8466 (p) cc_final: 0.8183 (p) REVERT: C 149 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7764 (mt) REVERT: C 255 ILE cc_start: 0.8577 (mt) cc_final: 0.8353 (mt) REVERT: C 257 LEU cc_start: 0.7328 (tp) cc_final: 0.6875 (tt) REVERT: C 259 GLN cc_start: 0.7476 (mt0) cc_final: 0.7125 (mt0) REVERT: C 261 ASP cc_start: 0.8280 (t0) cc_final: 0.7621 (t0) REVERT: D 161 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.7034 (t) REVERT: D 164 ASP cc_start: 0.5347 (m-30) cc_final: 0.4151 (m-30) REVERT: D 270 ASP cc_start: 0.7148 (m-30) cc_final: 0.6812 (t0) REVERT: D 327 TYR cc_start: 0.7629 (m-80) cc_final: 0.7305 (m-80) outliers start: 31 outliers final: 7 residues processed: 346 average time/residue: 0.1945 time to fit residues: 94.6744 Evaluate side-chains 211 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 202 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.0470 chunk 72 optimal weight: 0.0470 chunk 112 optimal weight: 2.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN D 139 ASN D 176 GLN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN D 357 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9631 Z= 0.264 Angle : 0.694 9.088 13119 Z= 0.365 Chirality : 0.046 0.165 1557 Planarity : 0.004 0.039 1640 Dihedral : 5.818 56.158 1337 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.71 % Favored : 96.88 % Rotamer: Outliers : 3.50 % Allowed : 18.33 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.32 (0.24), residues: 1216 helix: 2.37 (0.27), residues: 344 sheet: 0.91 (0.34), residues: 221 loop : -1.32 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 106 HIS 0.004 0.001 HIS C 125 PHE 0.019 0.002 PHE A 145 TYR 0.037 0.002 TYR D 157 ARG 0.006 0.001 ARG D 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 209 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TRP cc_start: 0.7943 (m-10) cc_final: 0.7681 (m-10) REVERT: A 322 GLN cc_start: 0.7111 (tt0) cc_final: 0.6897 (mp10) REVERT: B 215 MET cc_start: 0.8551 (tpp) cc_final: 0.8264 (tpp) REVERT: B 289 SER cc_start: 0.8548 (p) cc_final: 0.8249 (p) REVERT: C 149 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7855 (mt) REVERT: D 164 ASP cc_start: 0.5402 (m-30) cc_final: 0.4502 (m-30) REVERT: D 327 TYR cc_start: 0.7739 (m-80) cc_final: 0.7403 (m-80) outliers start: 34 outliers final: 26 residues processed: 233 average time/residue: 0.1767 time to fit residues: 60.2822 Evaluate side-chains 199 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 172 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 304 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 112 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 100 optimal weight: 0.0670 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN C 94 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN D 176 GLN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9631 Z= 0.196 Angle : 0.644 10.232 13119 Z= 0.337 Chirality : 0.044 0.176 1557 Planarity : 0.004 0.044 1640 Dihedral : 5.486 52.662 1333 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.12 % Favored : 96.46 % Rotamer: Outliers : 4.63 % Allowed : 19.46 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.24), residues: 1216 helix: 2.09 (0.27), residues: 344 sheet: 0.71 (0.34), residues: 239 loop : -1.27 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 106 HIS 0.002 0.001 HIS B 357 PHE 0.017 0.002 PHE C 141 TYR 0.022 0.001 TYR D 157 ARG 0.004 0.000 ARG C 272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 GLN cc_start: 0.7205 (tt0) cc_final: 0.6932 (mp10) REVERT: C 149 ILE cc_start: 0.8066 (mm) cc_final: 0.7734 (mt) REVERT: D 226 VAL cc_start: 0.9260 (t) cc_final: 0.8988 (p) REVERT: D 327 TYR cc_start: 0.7598 (m-80) cc_final: 0.7379 (m-80) outliers start: 45 outliers final: 29 residues processed: 225 average time/residue: 0.1669 time to fit residues: 55.6354 Evaluate side-chains 209 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 54.6181 > 50: distance: 30 - 31: 3.834 distance: 30 - 33: 7.908 distance: 31 - 32: 5.646 distance: 31 - 34: 5.076 distance: 34 - 35: 6.355 distance: 34 - 115: 9.762 distance: 35 - 36: 6.337 distance: 35 - 38: 10.243 distance: 36 - 37: 3.942 distance: 37 - 112: 12.709 distance: 38 - 39: 11.282 distance: 38 - 40: 4.868 distance: 41 - 163: 9.972 distance: 42 - 43: 19.585 distance: 42 - 45: 13.748 distance: 43 - 44: 9.731 distance: 43 - 49: 10.953 distance: 45 - 46: 10.053 distance: 45 - 47: 26.759 distance: 46 - 48: 25.864 distance: 49 - 50: 10.837 distance: 49 - 102: 13.247 distance: 50 - 51: 13.126 distance: 50 - 53: 12.150 distance: 51 - 52: 7.093 distance: 51 - 55: 7.605 distance: 52 - 99: 7.616 distance: 53 - 54: 10.942 distance: 56 - 57: 9.757 distance: 56 - 59: 9.472 distance: 57 - 58: 27.966 distance: 57 - 63: 12.436 distance: 59 - 60: 4.905 distance: 60 - 61: 10.672 distance: 61 - 62: 11.045 distance: 63 - 89: 15.976 distance: 64 - 65: 6.165 distance: 64 - 67: 8.676 distance: 65 - 66: 6.463 distance: 66 - 86: 12.781 distance: 67 - 68: 7.613 distance: 68 - 69: 8.773 distance: 69 - 70: 4.360 distance: 70 - 71: 4.881 distance: 71 - 72: 13.641 distance: 71 - 73: 6.487 distance: 74 - 75: 4.518 distance: 75 - 76: 9.194 distance: 75 - 78: 10.785 distance: 76 - 77: 15.309 distance: 76 - 82: 11.631 distance: 78 - 79: 8.876 distance: 79 - 80: 10.949 distance: 79 - 81: 9.306 distance: 83 - 84: 6.759 distance: 84 - 85: 6.510 distance: 84 - 86: 3.426 distance: 86 - 87: 6.903 distance: 87 - 88: 7.308 distance: 87 - 90: 3.032 distance: 88 - 89: 8.697 distance: 88 - 91: 4.877 distance: 91 - 92: 9.055 distance: 92 - 93: 6.976 distance: 92 - 95: 5.090 distance: 93 - 94: 7.702 distance: 93 - 99: 4.806 distance: 95 - 96: 4.865 distance: 96 - 97: 6.010 distance: 96 - 98: 5.034