Starting phenix.real_space_refine on Sat Aug 3 15:52:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uja_20794/08_2024/6uja_20794.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uja_20794/08_2024/6uja_20794.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/6uja_20794/08_2024/6uja_20794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uja_20794/08_2024/6uja_20794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uja_20794/08_2024/6uja_20794.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uja_20794/08_2024/6uja_20794.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= 0.003 sd= 0.077 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 Mg 1 5.21 5 S 32 5.16 5 C 5149 2.51 5 N 1419 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 171": "OD1" <-> "OD2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 228": "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: 8224 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4242 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 564} Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 200 Chain: "B" Number of atoms: 2811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2811 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 939 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 2 Unresolved non-hydrogen bonds: 507 Unresolved non-hydrogen angles: 652 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 297 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.53, per 1000 atoms: 0.67 Number of scatterers: 8224 At special positions: 0 Unit cell: (72.63, 100.875, 151.985, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 32 16.00 Mg 1 11.99 O 1618 8.00 N 1419 7.00 C 5149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.02 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.05 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.02 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 Links applied ALPHA1-2 " MAN C 4 " - " MAN C 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A2005 " - " ASN A 260 " " NAG B2005 " - " ASN B 360 " " NAG B2010 " - " ASN B 379 " " NAG C 1 " - " ASN A 266 " " NAG E 1 " - " ASN A 44 " " NAG F 1 " - " ASN B 191 " " NAG G 1 " - " ASN B 389 " " NAG H 1 " - " ASN B 414 " Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.6 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 18 sheets defined 15.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.971A pdb=" N SER B 126 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 250 through 256 Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.985A pdb=" N PHE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 115 removed outlier: 3.582A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 181 Processing helix chain 'D' and resid 215 through 224 removed outlier: 4.301A pdb=" N LEU D 218 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR D 220 " --> pdb=" O ASP D 217 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS D 222 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.277A pdb=" N THR A 412 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 423 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLY A 410 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY A 425 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N MET A 408 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 7.049A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.680A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.558A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.390A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 462 removed outlier: 7.217A pdb=" N LYS A 459 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS A 472 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N SER A 471 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 459 through 462 removed outlier: 7.217A pdb=" N LYS A 459 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS A 472 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.581A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N HIS B 422 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE B 83 " --> pdb=" O HIS B 422 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB7, first strand: chain 'B' and resid 182 through 189 removed outlier: 5.296A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ILE B 320 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE B 299 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 78 through 83 Processing sheet with id=AB9, first strand: chain 'D' and resid 101 through 107 removed outlier: 6.450A pdb=" N GLY D 187 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS D 144 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLN D 143 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR D 152 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR D 145 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP D 150 " --> pdb=" O TYR D 145 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 813 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: 2.68 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1905 1.32 - 1.45: 2186 1.45 - 1.58: 4232 1.58 - 1.71: 5 1.71 - 1.84: 50 Bond restraints: 8378 Sorted by residual: bond pdb=" CB HIS B 184 " pdb=" CG HIS B 184 " ideal model delta sigma weight residual 1.497 1.449 0.048 1.40e-02 5.10e+03 1.18e+01 bond pdb=" C5 NAG B2010 " pdb=" O5 NAG B2010 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C5 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" CG PHE A 1 " pdb=" CD1 PHE A 1 " ideal model delta sigma weight residual 1.384 1.453 -0.069 2.10e-02 2.27e+03 1.06e+01 ... (remaining 8373 not shown) Histogram of bond angle deviations from ideal: 99.84 - 112.88: 4564 112.88 - 125.93: 6771 125.93 - 138.98: 83 138.98 - 152.02: 0 152.02 - 165.07: 1 Bond angle restraints: 11419 Sorted by residual: angle pdb=" C2 NAG G 2 " pdb=" N2 NAG G 2 " pdb=" C7 NAG G 2 " ideal model delta sigma weight residual 124.56 165.07 -40.51 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C ALA A 362 " pdb=" N PRO A 363 " pdb=" CA PRO A 363 " ideal model delta sigma weight residual 119.56 127.75 -8.19 1.02e+00 9.61e-01 6.44e+01 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.28 128.09 -8.81 1.10e+00 8.26e-01 6.42e+01 angle pdb=" C GLY A 173 " pdb=" N PRO A 174 " pdb=" CA PRO A 174 " ideal model delta sigma weight residual 119.56 127.63 -8.07 1.01e+00 9.80e-01 6.38e+01 angle pdb=" C GLU D 117 " pdb=" N PRO D 118 " pdb=" CA PRO D 118 " ideal model delta sigma weight residual 119.87 128.01 -8.14 1.04e+00 9.25e-01 6.13e+01 ... (remaining 11414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 5075 21.38 - 42.75: 101 42.75 - 64.13: 26 64.13 - 85.50: 15 85.50 - 106.88: 6 Dihedral angle restraints: 5223 sinusoidal: 1985 harmonic: 3238 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 37.73 55.27 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS B 397 " pdb=" SG CYS B 397 " pdb=" SG CYS B 425 " pdb=" CB CYS B 425 " ideal model delta sinusoidal sigma weight residual -86.00 -118.26 32.26 1 1.00e+01 1.00e-02 1.48e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.17 106.88 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 5220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 941 0.072 - 0.143: 295 0.143 - 0.215: 59 0.215 - 0.287: 29 0.287 - 0.359: 18 Chirality restraints: 1342 Sorted by residual: chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.14e+01 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.27 0.13 2.00e-02 2.50e+03 4.26e+01 chirality pdb=" C1 MAN C 5 " pdb=" O2 MAN C 4 " pdb=" C2 MAN C 5 " pdb=" O5 MAN C 5 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 1.03e+01 ... (remaining 1339 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 260 " 0.030 2.00e-02 2.50e+03 3.08e-02 1.19e+01 pdb=" CG ASN A 260 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 260 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 260 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG A2005 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 44 " -0.029 2.00e-02 2.50e+03 3.07e-02 1.18e+01 pdb=" CG ASN A 44 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 44 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 44 " 0.048 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 172 " 0.043 2.00e-02 2.50e+03 2.24e-02 1.01e+01 pdb=" CG TYR B 172 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 172 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 172 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 172 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 172 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 172 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 172 " 0.032 2.00e-02 2.50e+03 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 29 2.42 - 3.04: 5151 3.04 - 3.66: 11604 3.66 - 4.28: 18614 4.28 - 4.90: 30127 Nonbonded interactions: 65525 Sorted by model distance: nonbonded pdb=" OD1 ASP D 217 " pdb="MG MG B2002 " model vdw 1.802 2.170 nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B2002 " model vdw 1.813 2.170 nonbonded pdb=" OG SER B 114 " pdb="MG MG B2002 " model vdw 1.973 2.170 nonbonded pdb=" OD1 ASP A 415 " pdb="CA CA A2003 " model vdw 2.088 2.510 nonbonded pdb=" OD1 ASP A 413 " pdb="CA CA A2003 " model vdw 2.096 2.510 ... (remaining 65520 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 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.014 0.083 8378 Z= 0.954 Angle : 1.487 40.507 11419 Z= 0.986 Chirality : 0.086 0.359 1342 Planarity : 0.006 0.033 1508 Dihedral : 11.587 106.875 3120 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.69 % Favored : 97.13 % Rotamer: Outliers : 0.14 % Allowed : 0.69 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.28 (0.24), residues: 1116 helix: -1.31 (0.37), residues: 132 sheet: 1.12 (0.24), residues: 384 loop : -0.01 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.007 TRP B 230 HIS 0.006 0.002 HIS B 63 PHE 0.026 0.004 PHE A 276 TYR 0.043 0.006 TYR B 172 ARG 0.004 0.001 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ASP cc_start: 0.7565 (t0) cc_final: 0.7257 (t0) REVERT: A 310 GLN cc_start: 0.7968 (mt0) cc_final: 0.7765 (mt0) REVERT: B 135 MET cc_start: 0.8261 (mmm) cc_final: 0.7916 (mmt) REVERT: B 173 ASN cc_start: 0.8626 (t0) cc_final: 0.8402 (t0) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.2784 time to fit residues: 47.2887 Evaluate side-chains 61 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8378 Z= 0.328 Angle : 0.660 8.518 11419 Z= 0.357 Chirality : 0.048 0.192 1342 Planarity : 0.004 0.032 1508 Dihedral : 8.075 86.998 1541 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.69 % Favored : 97.22 % Rotamer: Outliers : 1.25 % Allowed : 6.93 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.39 (0.24), residues: 1116 helix: -0.11 (0.45), residues: 126 sheet: 0.87 (0.24), residues: 407 loop : -0.00 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 179 HIS 0.004 0.001 HIS A 113 PHE 0.018 0.002 PHE A 276 TYR 0.017 0.002 TYR A 112 ARG 0.007 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.6818 (mm-40) cc_final: 0.6594 (mp-120) REVERT: A 146 ASP cc_start: 0.8286 (t0) cc_final: 0.7878 (t0) REVERT: B 135 MET cc_start: 0.8417 (mmm) cc_final: 0.7996 (mmt) REVERT: B 173 ASN cc_start: 0.8701 (t0) cc_final: 0.8484 (t0) REVERT: B 345 GLU cc_start: 0.6751 (tt0) cc_final: 0.6524 (tt0) outliers start: 9 outliers final: 5 residues processed: 80 average time/residue: 0.2087 time to fit residues: 23.2697 Evaluate side-chains 64 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 0.3980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8378 Z= 0.239 Angle : 0.564 5.285 11419 Z= 0.302 Chirality : 0.047 0.247 1342 Planarity : 0.004 0.033 1508 Dihedral : 6.964 72.249 1541 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.08 % Allowed : 6.09 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.27 (0.25), residues: 1116 helix: 0.20 (0.48), residues: 127 sheet: 0.62 (0.24), residues: 420 loop : -0.06 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 179 HIS 0.004 0.001 HIS B 161 PHE 0.014 0.002 PHE A 276 TYR 0.014 0.002 TYR A 112 ARG 0.006 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: B 173 ASN cc_start: 0.8627 (t0) cc_final: 0.8419 (t0) outliers start: 15 outliers final: 8 residues processed: 72 average time/residue: 0.1965 time to fit residues: 20.3343 Evaluate side-chains 64 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 chunk 60 optimal weight: 0.0770 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8378 Z= 0.309 Angle : 0.583 5.773 11419 Z= 0.305 Chirality : 0.048 0.253 1342 Planarity : 0.004 0.046 1508 Dihedral : 6.693 63.795 1541 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.08 % Allowed : 7.48 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.09 (0.24), residues: 1116 helix: 0.07 (0.48), residues: 127 sheet: 0.62 (0.24), residues: 411 loop : -0.28 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 179 HIS 0.005 0.001 HIS B 161 PHE 0.016 0.002 PHE A 326 TYR 0.017 0.002 TYR A 112 ARG 0.003 0.001 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASP cc_start: 0.8335 (t0) cc_final: 0.8034 (t0) REVERT: A 275 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8482 (t80) REVERT: B 103 TYR cc_start: 0.8802 (m-80) cc_final: 0.8477 (m-80) REVERT: B 173 ASN cc_start: 0.8719 (t0) cc_final: 0.8295 (t0) outliers start: 15 outliers final: 8 residues processed: 69 average time/residue: 0.2069 time to fit residues: 20.2541 Evaluate side-chains 67 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8378 Z= 0.327 Angle : 0.590 8.477 11419 Z= 0.308 Chirality : 0.048 0.259 1342 Planarity : 0.004 0.037 1508 Dihedral : 6.550 59.052 1541 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.22 % Allowed : 8.73 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.01 (0.24), residues: 1116 helix: 0.02 (0.48), residues: 127 sheet: 0.57 (0.24), residues: 414 loop : -0.37 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 179 HIS 0.007 0.001 HIS D 222 PHE 0.015 0.002 PHE A 276 TYR 0.017 0.002 TYR A 112 ARG 0.005 0.001 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8439 (t80) REVERT: B 103 TYR cc_start: 0.8949 (m-80) cc_final: 0.8619 (m-80) REVERT: B 173 ASN cc_start: 0.8762 (t0) cc_final: 0.8335 (t0) outliers start: 16 outliers final: 10 residues processed: 74 average time/residue: 0.2228 time to fit residues: 23.2099 Evaluate side-chains 72 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8378 Z= 0.307 Angle : 0.567 5.979 11419 Z= 0.296 Chirality : 0.048 0.257 1342 Planarity : 0.004 0.036 1508 Dihedral : 6.456 54.911 1541 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.35 % Allowed : 9.28 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.05 (0.24), residues: 1116 helix: -0.06 (0.48), residues: 128 sheet: 0.57 (0.24), residues: 407 loop : -0.40 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 230 HIS 0.005 0.001 HIS D 222 PHE 0.014 0.002 PHE A 276 TYR 0.016 0.002 TYR A 112 ARG 0.004 0.001 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8428 (t80) REVERT: B 103 TYR cc_start: 0.8943 (m-80) cc_final: 0.8564 (m-80) REVERT: B 173 ASN cc_start: 0.8696 (t0) cc_final: 0.8313 (t0) outliers start: 17 outliers final: 11 residues processed: 74 average time/residue: 0.2090 time to fit residues: 21.9348 Evaluate side-chains 73 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.1799 > 50: distance: 14 - 17: 6.925 distance: 17 - 18: 6.695 distance: 18 - 19: 9.616 distance: 18 - 21: 11.904 distance: 19 - 20: 23.893 distance: 19 - 22: 11.370 distance: 22 - 23: 17.547 distance: 23 - 24: 10.814 distance: 23 - 26: 10.397 distance: 24 - 25: 14.053 distance: 24 - 30: 10.762 distance: 26 - 27: 19.856 distance: 26 - 28: 17.505 distance: 27 - 29: 20.481 distance: 30 - 31: 15.431 distance: 31 - 32: 5.597 distance: 31 - 34: 21.472 distance: 32 - 33: 19.736 distance: 32 - 38: 24.395 distance: 34 - 35: 27.371 distance: 35 - 36: 21.990 distance: 35 - 37: 22.344 distance: 38 - 39: 31.563 distance: 39 - 40: 9.573 distance: 39 - 42: 8.970 distance: 40 - 41: 20.456 distance: 40 - 45: 23.472 distance: 42 - 43: 16.343 distance: 42 - 44: 3.240 distance: 45 - 46: 9.947 distance: 46 - 47: 7.380 distance: 46 - 49: 30.108 distance: 47 - 48: 36.164 distance: 47 - 54: 8.401 distance: 49 - 50: 46.454 distance: 50 - 51: 25.862 distance: 51 - 52: 20.911 distance: 51 - 53: 22.264 distance: 54 - 55: 20.175 distance: 55 - 56: 27.860 distance: 55 - 58: 28.122 distance: 56 - 57: 18.473 distance: 56 - 61: 22.470 distance: 58 - 59: 32.293 distance: 58 - 60: 27.200 distance: 61 - 62: 45.726 distance: 61 - 109: 20.850 distance: 62 - 63: 21.356 distance: 62 - 65: 32.473 distance: 63 - 64: 5.367 distance: 63 - 68: 37.540 distance: 64 - 106: 27.292 distance: 65 - 66: 50.556 distance: 65 - 67: 47.188 distance: 68 - 69: 33.165 distance: 68 - 74: 22.579 distance: 69 - 70: 34.383 distance: 69 - 72: 20.913 distance: 70 - 71: 21.198 distance: 70 - 75: 15.432 distance: 72 - 73: 48.608 distance: 73 - 74: 18.480 distance: 75 - 76: 51.541 distance: 76 - 77: 31.277 distance: 77 - 78: 38.973 distance: 77 - 79: 29.793 distance: 79 - 80: 18.700 distance: 80 - 81: 12.790 distance: 80 - 83: 34.885 distance: 81 - 88: 21.982 distance: 83 - 84: 10.974 distance: 84 - 85: 20.669 distance: 85 - 86: 19.567 distance: 85 - 87: 12.588