Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 19:21:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uja_20794/04_2023/6uja_20794.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uja_20794/04_2023/6uja_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_20794/04_2023/6uja_20794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uja_20794/04_2023/6uja_20794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uja_20794/04_2023/6uja_20794.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uja_20794/04_2023/6uja_20794.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 4.82, per 1000 atoms: 0.59 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: 3.58 Conformation dependent library (CDL) restraints added in 1.2 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: 0.61 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: 2.72 Time building geometry restraints manager: 3.87 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 - 17.77: 4713 17.77 - 35.54: 113 35.54 - 53.30: 26 53.30 - 71.07: 14 71.07 - 88.84: 8 Dihedral angle restraints: 4874 sinusoidal: 1636 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=" CA TYR B 103 " pdb=" C TYR B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 4871 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 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: 1.730 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: 6.090 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.180 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- 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 : 10.456 88.842 2771 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 % 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 *********************** 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 : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.2914 time to fit residues: 49.8115 Evaluate side-chains 59 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2843 ------------------------------------------------------------------------------- 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: 0.7980 chunk 84 optimal weight: 0.0670 chunk 46 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN ** B 302 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: 0.8023 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 8378 Z= 0.258 Angle : 0.618 8.829 11419 Z= 0.334 Chirality : 0.047 0.169 1342 Planarity : 0.004 0.028 1508 Dihedral : 4.765 21.557 1192 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.78 % Favored : 97.13 % Rotamer Outliers : 1.52 % 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: 0.43 (0.25), residues: 1116 helix: -0.04 (0.46), residues: 126 sheet: 0.87 (0.24), residues: 401 loop : 0.04 (0.26), residues: 589 *********************** 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: 11 poor density : 72 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 80 average time/residue: 0.2159 time to fit residues: 24.2333 Evaluate side-chains 63 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1522 time to fit residues: 2.5921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.8160 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 8378 Z= 0.477 Angle : 0.674 6.028 11419 Z= 0.355 Chirality : 0.050 0.151 1342 Planarity : 0.005 0.036 1508 Dihedral : 4.812 17.205 1192 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 2.22 % 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 (0.25), residues: 1116 helix: -0.13 (0.47), residues: 126 sheet: 0.57 (0.24), residues: 414 loop : -0.24 (0.26), residues: 576 *********************** 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 77 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 70 average time/residue: 0.2024 time to fit residues: 20.5289 Evaluate side-chains 64 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0816 time to fit residues: 2.3125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 101 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 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 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: 0.8134 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 8378 Z= 0.270 Angle : 0.554 5.435 11419 Z= 0.291 Chirality : 0.046 0.152 1342 Planarity : 0.004 0.035 1508 Dihedral : 4.478 16.306 1192 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.11 % 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: 0.02 (0.25), residues: 1116 helix: -0.06 (0.49), residues: 127 sheet: 0.59 (0.24), residues: 413 loop : -0.32 (0.26), residues: 576 *********************** 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 70 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.853 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 67 average time/residue: 0.2448 time to fit residues: 22.5892 Evaluate side-chains 61 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2452 time to fit residues: 2.3086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN D 222 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.055 8378 Z= 0.519 Angle : 0.687 7.224 11419 Z= 0.355 Chirality : 0.050 0.180 1342 Planarity : 0.005 0.047 1508 Dihedral : 4.799 20.759 1192 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 1.66 % 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: -0.35 (0.24), residues: 1116 helix: -0.36 (0.47), residues: 126 sheet: 0.38 (0.24), residues: 409 loop : -0.58 (0.25), residues: 581 *********************** 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 77 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 70 average time/residue: 0.2250 time to fit residues: 22.1386 Evaluate side-chains 65 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0902 time to fit residues: 2.0245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 0.0570 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN B 202 GLN D 222 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8378 Z= 0.226 Angle : 0.542 5.746 11419 Z= 0.283 Chirality : 0.045 0.142 1342 Planarity : 0.004 0.032 1508 Dihedral : 4.379 17.977 1192 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.97 % 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: -0.12 (0.24), residues: 1116 helix: -0.10 (0.48), residues: 127 sheet: 0.55 (0.24), residues: 412 loop : -0.48 (0.26), residues: 577 *********************** 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 72 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 67 average time/residue: 0.2348 time to fit residues: 22.0089 Evaluate side-chains 62 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3341 time to fit residues: 2.1115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 0.4980 chunk 65 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 0.0010 chunk 32 optimal weight: 1.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN D 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 8378 Z= 0.180 Angle : 0.507 5.655 11419 Z= 0.266 Chirality : 0.045 0.172 1342 Planarity : 0.003 0.032 1508 Dihedral : 4.117 15.648 1192 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.83 % 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: 0.07 (0.25), residues: 1116 helix: 0.26 (0.50), residues: 127 sheet: 0.77 (0.25), residues: 407 loop : -0.49 (0.25), residues: 582 *********************** REFINEMENT MACRO_CYCLE 7 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 74 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 72 average time/residue: 0.2010 time to fit residues: 21.1688 Evaluate side-chains 66 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0964 time to fit residues: 1.2878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.0970 chunk 84 optimal weight: 0.5980 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 8378 Z= 0.257 Angle : 0.552 6.052 11419 Z= 0.288 Chirality : 0.046 0.165 1342 Planarity : 0.004 0.029 1508 Dihedral : 4.189 16.067 1192 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.97 % 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 (0.25), residues: 1116 helix: 0.46 (0.51), residues: 120 sheet: 0.77 (0.25), residues: 410 loop : -0.51 (0.25), residues: 586 *********************** REFINEMENT MACRO_CYCLE 8 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 72 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 68 average time/residue: 0.1990 time to fit residues: 19.7392 Evaluate side-chains 61 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0870 time to fit residues: 1.4146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 0.0670 chunk 105 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8378 Z= 0.220 Angle : 0.541 6.381 11419 Z= 0.283 Chirality : 0.045 0.205 1342 Planarity : 0.004 0.029 1508 Dihedral : 4.101 15.386 1192 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.69 % 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: 0.16 (0.25), residues: 1116 helix: 0.56 (0.52), residues: 120 sheet: 0.83 (0.25), residues: 410 loop : -0.49 (0.25), residues: 586 *********************** REFINEMENT MACRO_CYCLE 9 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 67 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 0.1925 time to fit residues: 18.3647 Evaluate side-chains 61 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0896 time to fit residues: 1.4636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 40.0000 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 0.0770 chunk 26 optimal weight: 0.5980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8378 Z= 0.264 Angle : 0.565 7.544 11419 Z= 0.295 Chirality : 0.046 0.198 1342 Planarity : 0.004 0.029 1508 Dihedral : 4.172 15.691 1192 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.14 % 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: 0.11 (0.25), residues: 1116 helix: 0.45 (0.51), residues: 120 sheet: 0.81 (0.25), residues: 410 loop : -0.52 (0.25), residues: 586 ********************** REFINEMENT MACRO_CYCLE 10 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 62 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.2234 time to fit residues: 19.6603 Evaluate side-chains 59 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.0770 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.129198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095122 restraints weight = 13210.511| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.32 r_work: 0.3048 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8378 Z= 0.224 Angle : 0.538 6.313 11419 Z= 0.281 Chirality : 0.045 0.194 1342 Planarity : 0.004 0.038 1508 Dihedral : 4.085 15.123 1192 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.55 % 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: 0.13 (0.25), residues: 1116 helix: 0.55 (0.51), residues: 120 sheet: 0.82 (0.25), residues: 410 loop : -0.52 (0.25), residues: 586 =============================================================================== Job complete usr+sys time: 1734.57 seconds wall clock time: 32 minutes 4.49 seconds (1924.49 seconds total)