Starting phenix.real_space_refine on Wed Mar 12 22:11:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1t_33572/03_2025/7y1t_33572.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1t_33572/03_2025/7y1t_33572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y1t_33572/03_2025/7y1t_33572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1t_33572/03_2025/7y1t_33572.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1t_33572/03_2025/7y1t_33572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1t_33572/03_2025/7y1t_33572.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.047 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 Mn 1 7.51 5 S 38 5.16 5 C 5127 2.51 5 N 1357 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8112 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4114 Classifications: {'peptide': 534} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 507} Chain breaks: 3 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2714 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Chain: "D" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1038 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 131 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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: "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: "G" 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: "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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 1, ' MN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.71, per 1000 atoms: 0.70 Number of scatterers: 8112 At special positions: 0 Unit cell: (100.225, 75.96, 150.865, 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) Mn 1 24.99 Ca 5 19.99 S 38 16.00 O 1584 8.00 N 1357 7.00 C 5127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 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 A 401 " - pdb=" SG CYS B 259 " distance=2.04 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 536 " 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-3 " BMA G 3 " - " MAN G 6 " ALPHA1-4 " BMA G 3 " - " MAN G 4 " ALPHA1-6 " MAN G 4 " - " MAN G 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 701 " - " ASN A 525 " " NAG B 501 " - " ASN B 389 " " NAG B 502 " - " ASN B 191 " " NAG B 503 " - " ASN B 360 " " NAG C 1 " - " ASN A 260 " " NAG D 401 " - " ASN D 107 " " NAG E 1 " - " ASN A 44 " " NAG F 1 " - " ASN B 414 " " NAG G 1 " - " ASN A 266 " Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 962.3 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 18 sheets defined 14.3% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 147 through 152 removed outlier: 4.459A pdb=" N GLY A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 152' 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 removed outlier: 3.609A pdb=" N THR A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.816A pdb=" N HIS B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 126 through 136 removed outlier: 3.985A pdb=" N ASP B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 192 through 202 removed outlier: 3.770A pdb=" N HIS B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 248 through 254 removed outlier: 4.083A pdb=" N SER B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 254 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 330 through 345 Processing helix chain 'D' and resid 107 through 115 removed outlier: 3.989A pdb=" N LEU D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 180 removed outlier: 4.020A pdb=" N SER D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.921A pdb=" N ASP A 422 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 412 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 408 " --> pdb=" O GLY A 426 " (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: 4.016A pdb=" N ALA A 81 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 removed outlier: 4.046A pdb=" N HIS A 113 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.958A pdb=" N SER A 97 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.754A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.598A 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 Processing sheet with id=AA8, first strand: chain 'A' and resid 279 through 283 removed outlier: 4.020A pdb=" N SER A 279 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 293 " --> pdb=" O SER A 318 " (cutoff:3.500A) 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 343 through 348 removed outlier: 6.330A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 537 through 539 removed outlier: 3.737A pdb=" N GLU A 537 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 478 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL A 476 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 524 through 529 removed outlier: 4.043A pdb=" N LYS A 524 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 496 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 528 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 492 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.669A pdb=" N HIS B 422 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 407 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 409 " --> pdb=" O GLN B 349 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 97 removed outlier: 3.566A pdb=" N VAL B 392 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 390 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 95 " --> pdb=" O PHE B 388 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 393 " --> pdb=" O TYR B 358 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 91 through 97 removed outlier: 3.566A pdb=" N VAL B 392 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 390 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 95 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 183 through 189 removed outlier: 6.411A pdb=" N VAL B 185 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N SER B 148 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER B 187 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE B 146 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 109 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 111 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 149 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP B 106 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU B 239 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR B 108 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET B 241 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 110 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 296 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.052A pdb=" N PHE D 228 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 127 " --> pdb=" O PHE D 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 102 through 106 removed outlier: 3.746A pdb=" N ILE D 102 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 190 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET D 104 " --> pdb=" O PHE D 188 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY D 187 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 144 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 139 " --> pdb=" O ARG D 156 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG D 156 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU D 141 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER D 154 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN D 143 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR D 152 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR D 145 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP D 150 " --> pdb=" O TYR D 145 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 594 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: 2.41 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2645 1.34 - 1.46: 1943 1.46 - 1.58: 3630 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 8278 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1 MAN G 4 " pdb=" C2 MAN G 4 " ideal model delta sigma weight residual 1.526 1.566 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C1 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.399 1.434 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C1 MAN G 6 " pdb=" C2 MAN G 6 " ideal model delta sigma weight residual 1.526 1.558 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 NAG F 3 " pdb=" O5 NAG F 3 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 8273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 10800 1.31 - 2.63: 318 2.63 - 3.94: 81 3.94 - 5.26: 20 5.26 - 6.57: 11 Bond angle restraints: 11230 Sorted by residual: angle pdb=" C ASP A 288 " pdb=" N ASP A 289 " pdb=" CA ASP A 289 " ideal model delta sigma weight residual 124.31 130.49 -6.18 1.67e+00 3.59e-01 1.37e+01 angle pdb=" C SER A 201 " pdb=" N ILE A 202 " pdb=" CA ILE A 202 " ideal model delta sigma weight residual 121.97 126.30 -4.33 1.80e+00 3.09e-01 5.80e+00 angle pdb=" CA ASP A 289 " pdb=" CB ASP A 289 " pdb=" CG ASP A 289 " ideal model delta sigma weight residual 112.60 114.90 -2.30 1.00e+00 1.00e+00 5.27e+00 angle pdb=" CA CYS B 259 " pdb=" CB CYS B 259 " pdb=" SG CYS B 259 " ideal model delta sigma weight residual 114.40 119.52 -5.12 2.30e+00 1.89e-01 4.96e+00 angle pdb=" C PHE B 195 " pdb=" N GLU B 196 " pdb=" CA GLU B 196 " ideal model delta sigma weight residual 120.31 117.19 3.12 1.52e+00 4.33e-01 4.21e+00 ... (remaining 11225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 4778 22.77 - 45.55: 283 45.55 - 68.32: 58 68.32 - 91.10: 20 91.10 - 113.87: 19 Dihedral angle restraints: 5158 sinusoidal: 2207 harmonic: 2951 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 -86.00 -38.55 -47.45 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" CB CYS A 401 " pdb=" SG CYS A 401 " pdb=" SG CYS B 259 " pdb=" CB CYS B 259 " ideal model delta sinusoidal sigma weight residual -86.00 -126.14 40.14 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA ALA B 329 " pdb=" C ALA B 329 " pdb=" N ASN B 330 " pdb=" CA ASN B 330 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.316: 1286 0.316 - 0.633: 2 0.633 - 0.949: 1 0.949 - 1.266: 0 1.266 - 1.582: 3 Chirality restraints: 1292 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-02 2.50e+03 5.47e+02 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 266 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.82 -1.58 2.00e-01 2.50e+01 6.26e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 414 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.95 -1.45 2.00e-01 2.50e+01 5.28e+01 ... (remaining 1289 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 266 " -0.163 2.00e-02 2.50e+03 2.04e-01 5.21e+02 pdb=" CG ASN A 266 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN A 266 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 266 " 0.340 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.248 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 414 " -0.152 2.00e-02 2.50e+03 1.93e-01 4.67e+02 pdb=" CG ASN B 414 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN B 414 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 414 " 0.325 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 525 " -0.115 2.00e-02 2.50e+03 1.34e-01 2.23e+02 pdb=" CG ASN A 525 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 525 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 525 " 0.217 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.163 2.00e-02 2.50e+03 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 88 2.58 - 3.16: 6368 3.16 - 3.74: 11799 3.74 - 4.32: 16459 4.32 - 4.90: 27765 Nonbonded interactions: 62479 Sorted by model distance: nonbonded pdb=" OD1 ASP D 217 " pdb="MN MN B 505 " model vdw 1.998 2.320 nonbonded pdb=" OG SER A 144 " pdb=" OD1 ASP A 146 " model vdw 2.130 3.040 nonbonded pdb=" NZ LYS B 327 " pdb=" O ALA B 329 " model vdw 2.182 3.120 nonbonded pdb=" OD1 ASP B 130 " pdb=" ND2 ASN B 332 " model vdw 2.190 3.120 nonbonded pdb=" OD1 ASP A 24 " pdb=" N PHE A 25 " model vdw 2.233 3.120 ... (remaining 62474 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 'C' selection = chain 'E' } 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: 59.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.120 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 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 : 0.003 0.083 8278 Z= 0.214 Angle : 0.588 6.573 11230 Z= 0.277 Chirality : 0.087 1.582 1292 Planarity : 0.004 0.104 1449 Dihedral : 16.885 113.873 3244 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.76 (0.27), residues: 1014 helix: 1.39 (0.57), residues: 98 sheet: 0.21 (0.29), residues: 337 loop : -1.33 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.002 0.000 HIS A 113 PHE 0.017 0.001 PHE B 137 TYR 0.011 0.001 TYR A 200 ARG 0.005 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 474 PHE cc_start: 0.3816 (p90) cc_final: 0.3565 (p90) REVERT: B 250 LEU cc_start: 0.8421 (mt) cc_final: 0.8081 (mt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2094 time to fit residues: 36.8342 Evaluate side-chains 87 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.132476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.104762 restraints weight = 14098.591| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.93 r_work: 0.3444 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8278 Z= 0.271 Angle : 0.663 9.531 11230 Z= 0.321 Chirality : 0.048 0.275 1292 Planarity : 0.004 0.078 1449 Dihedral : 12.284 96.129 1472 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.22 % Allowed : 10.34 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.69 (0.27), residues: 1014 helix: 1.74 (0.56), residues: 100 sheet: -0.02 (0.27), residues: 373 loop : -1.21 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.004 0.001 HIS A 113 PHE 0.029 0.002 PHE B 137 TYR 0.013 0.002 TYR A 178 ARG 0.005 0.001 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7003 (p0) REVERT: A 474 PHE cc_start: 0.3557 (p90) cc_final: 0.3303 (p90) REVERT: B 224 CYS cc_start: 0.7716 (m) cc_final: 0.7475 (m) outliers start: 10 outliers final: 7 residues processed: 97 average time/residue: 0.2636 time to fit residues: 35.8152 Evaluate side-chains 88 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.129024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.101144 restraints weight = 14192.453| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.92 r_work: 0.3386 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8278 Z= 0.221 Angle : 0.621 15.479 11230 Z= 0.300 Chirality : 0.048 0.305 1292 Planarity : 0.004 0.056 1449 Dihedral : 10.360 94.138 1472 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.58 % Allowed : 13.02 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.68 (0.27), residues: 1014 helix: 1.83 (0.58), residues: 96 sheet: -0.06 (0.27), residues: 374 loop : -1.15 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 61 HIS 0.004 0.001 HIS A 113 PHE 0.022 0.001 PHE B 137 TYR 0.014 0.001 TYR A 420 ARG 0.003 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.914 Fit side-chains REVERT: A 108 CYS cc_start: 0.7109 (m) cc_final: 0.6665 (m) REVERT: A 474 PHE cc_start: 0.3620 (p90) cc_final: 0.3289 (p90) REVERT: B 141 ASP cc_start: 0.7709 (t0) cc_final: 0.6455 (p0) REVERT: B 224 CYS cc_start: 0.7666 (m) cc_final: 0.7459 (m) outliers start: 13 outliers final: 6 residues processed: 90 average time/residue: 0.2359 time to fit residues: 29.6535 Evaluate side-chains 81 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain D residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 0.0970 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.126731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.098836 restraints weight = 14024.406| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.90 r_work: 0.3352 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8278 Z= 0.248 Angle : 0.619 13.701 11230 Z= 0.301 Chirality : 0.047 0.301 1292 Planarity : 0.004 0.050 1449 Dihedral : 9.893 91.587 1472 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.43 % Allowed : 13.87 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.74 (0.27), residues: 1014 helix: 1.67 (0.57), residues: 100 sheet: -0.19 (0.27), residues: 374 loop : -1.12 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.002 0.001 HIS A 113 PHE 0.019 0.001 PHE B 137 TYR 0.011 0.001 TYR A 562 ARG 0.004 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.908 Fit side-chains REVERT: A 60 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7087 (p0) REVERT: A 368 ASP cc_start: 0.8156 (t0) cc_final: 0.7864 (t0) REVERT: A 474 PHE cc_start: 0.3099 (p90) cc_final: 0.2849 (p90) REVERT: B 141 ASP cc_start: 0.7650 (t0) cc_final: 0.6450 (p0) REVERT: B 224 CYS cc_start: 0.7599 (m) cc_final: 0.7376 (m) outliers start: 20 outliers final: 13 residues processed: 92 average time/residue: 0.1927 time to fit residues: 25.0458 Evaluate side-chains 90 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain D residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.125973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098071 restraints weight = 13908.487| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.88 r_work: 0.3338 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8278 Z= 0.225 Angle : 0.603 13.477 11230 Z= 0.291 Chirality : 0.046 0.295 1292 Planarity : 0.004 0.047 1449 Dihedral : 9.611 90.868 1472 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.95 % Allowed : 16.18 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.27), residues: 1014 helix: 1.57 (0.56), residues: 102 sheet: -0.18 (0.27), residues: 373 loop : -1.10 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.002 0.001 HIS A 113 PHE 0.018 0.001 PHE B 137 TYR 0.012 0.001 TYR A 420 ARG 0.003 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.957 Fit side-chains REVERT: A 60 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7306 (p0) REVERT: A 368 ASP cc_start: 0.8187 (t0) cc_final: 0.7825 (t0) REVERT: A 474 PHE cc_start: 0.3123 (p90) cc_final: 0.2886 (p90) REVERT: B 141 ASP cc_start: 0.7633 (t0) cc_final: 0.6417 (p0) outliers start: 16 outliers final: 10 residues processed: 93 average time/residue: 0.1861 time to fit residues: 24.7175 Evaluate side-chains 88 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain D residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 94 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.123687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.095559 restraints weight = 14197.117| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.91 r_work: 0.3293 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8278 Z= 0.296 Angle : 0.637 12.736 11230 Z= 0.311 Chirality : 0.047 0.295 1292 Planarity : 0.004 0.048 1449 Dihedral : 9.520 89.344 1472 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.92 % Allowed : 15.94 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.78 (0.27), residues: 1014 helix: 1.50 (0.56), residues: 102 sheet: -0.28 (0.27), residues: 372 loop : -1.07 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.027 0.002 PHE B 137 TYR 0.013 0.001 TYR A 420 ARG 0.003 0.000 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7112 (p0) REVERT: A 368 ASP cc_start: 0.8295 (t0) cc_final: 0.7905 (t0) REVERT: A 474 PHE cc_start: 0.3183 (p90) cc_final: 0.2935 (p90) REVERT: A 483 ASP cc_start: 0.7214 (t70) cc_final: 0.6965 (t70) outliers start: 24 outliers final: 17 residues processed: 95 average time/residue: 0.1847 time to fit residues: 25.0688 Evaluate side-chains 93 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 234 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.124153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096150 restraints weight = 14140.834| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.90 r_work: 0.3300 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8278 Z= 0.227 Angle : 0.610 13.646 11230 Z= 0.297 Chirality : 0.047 0.289 1292 Planarity : 0.004 0.048 1449 Dihedral : 9.393 89.277 1472 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.92 % Allowed : 16.67 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.72 (0.27), residues: 1014 helix: 1.52 (0.56), residues: 102 sheet: -0.20 (0.27), residues: 372 loop : -1.06 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 61 HIS 0.002 0.001 HIS B 307 PHE 0.026 0.001 PHE B 137 TYR 0.011 0.001 TYR A 562 ARG 0.003 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7116 (p0) REVERT: A 225 SER cc_start: 0.8753 (t) cc_final: 0.8485 (p) REVERT: A 275 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: A 368 ASP cc_start: 0.8311 (t0) cc_final: 0.7913 (t0) REVERT: A 474 PHE cc_start: 0.3132 (p90) cc_final: 0.2855 (p90) REVERT: A 483 ASP cc_start: 0.7346 (t70) cc_final: 0.7029 (t70) REVERT: D 140 GLU cc_start: 0.6029 (OUTLIER) cc_final: 0.5596 (tp30) outliers start: 24 outliers final: 17 residues processed: 97 average time/residue: 0.1817 time to fit residues: 25.3421 Evaluate side-chains 98 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 140 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 0.0010 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.096333 restraints weight = 14282.114| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.79 r_work: 0.3307 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8278 Z= 0.229 Angle : 0.606 13.150 11230 Z= 0.295 Chirality : 0.047 0.287 1292 Planarity : 0.004 0.049 1449 Dihedral : 9.285 88.518 1472 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.55 % Allowed : 17.64 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.71 (0.27), residues: 1014 helix: 1.52 (0.56), residues: 102 sheet: -0.19 (0.27), residues: 372 loop : -1.04 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.002 0.001 HIS B 307 PHE 0.025 0.001 PHE B 137 TYR 0.010 0.001 TYR A 562 ARG 0.003 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7728 (t70) cc_final: 0.7138 (p0) REVERT: A 225 SER cc_start: 0.8765 (t) cc_final: 0.8509 (p) REVERT: A 275 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: A 368 ASP cc_start: 0.8302 (t0) cc_final: 0.7913 (t0) REVERT: A 409 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8659 (ptp) REVERT: A 474 PHE cc_start: 0.3298 (p90) cc_final: 0.3016 (p90) REVERT: A 483 ASP cc_start: 0.7324 (t70) cc_final: 0.7080 (t70) REVERT: D 140 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5613 (tp30) outliers start: 21 outliers final: 14 residues processed: 96 average time/residue: 0.2118 time to fit residues: 30.5881 Evaluate side-chains 96 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 140 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.122296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.094494 restraints weight = 14540.255| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.82 r_work: 0.3274 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8278 Z= 0.272 Angle : 0.633 11.858 11230 Z= 0.311 Chirality : 0.048 0.289 1292 Planarity : 0.004 0.050 1449 Dihedral : 9.236 87.348 1472 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.80 % Allowed : 18.13 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.72 (0.27), residues: 1014 helix: 1.44 (0.56), residues: 103 sheet: -0.23 (0.27), residues: 372 loop : -1.02 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.024 0.002 PHE B 137 TYR 0.013 0.002 TYR A 178 ARG 0.003 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: A 225 SER cc_start: 0.8787 (t) cc_final: 0.8540 (p) REVERT: A 275 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: A 368 ASP cc_start: 0.8348 (t0) cc_final: 0.8107 (t0) REVERT: A 409 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8634 (ptp) REVERT: A 497 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6678 (pp20) REVERT: D 140 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5841 (tp30) outliers start: 23 outliers final: 18 residues processed: 97 average time/residue: 0.2876 time to fit residues: 41.1964 Evaluate side-chains 97 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 222 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 0.0570 chunk 73 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.122889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094978 restraints weight = 14178.240| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.87 r_work: 0.3283 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8278 Z= 0.232 Angle : 0.621 11.453 11230 Z= 0.303 Chirality : 0.047 0.286 1292 Planarity : 0.004 0.051 1449 Dihedral : 9.195 87.584 1472 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.31 % Allowed : 18.37 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.72 (0.27), residues: 1014 helix: 1.47 (0.56), residues: 103 sheet: -0.25 (0.27), residues: 372 loop : -1.01 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.024 0.001 PHE B 137 TYR 0.012 0.001 TYR A 178 ARG 0.002 0.000 ARG D 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 225 SER cc_start: 0.8792 (t) cc_final: 0.8536 (p) REVERT: A 275 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: A 368 ASP cc_start: 0.8508 (t0) cc_final: 0.8120 (t0) REVERT: A 409 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8643 (ptp) REVERT: A 497 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6678 (pp20) REVERT: D 140 GLU cc_start: 0.6231 (tp30) cc_final: 0.5796 (tp30) outliers start: 19 outliers final: 16 residues processed: 91 average time/residue: 0.1874 time to fit residues: 24.3334 Evaluate side-chains 93 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 222 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.096622 restraints weight = 14237.738| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.87 r_work: 0.3309 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8278 Z= 0.181 Angle : 0.594 10.377 11230 Z= 0.287 Chirality : 0.046 0.280 1292 Planarity : 0.004 0.051 1449 Dihedral : 8.984 86.528 1472 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.43 % Allowed : 18.49 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.62 (0.27), residues: 1014 helix: 1.59 (0.56), residues: 103 sheet: -0.10 (0.27), residues: 361 loop : -1.01 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 61 HIS 0.002 0.001 HIS B 307 PHE 0.023 0.001 PHE B 137 TYR 0.012 0.001 TYR A 562 ARG 0.002 0.000 ARG A 398 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4087.01 seconds wall clock time: 73 minutes 23.47 seconds (4403.47 seconds total)