Starting phenix.real_space_refine on Thu Jul 2 10:31:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y1t_33572/07_2026/7y1t_33572.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1t_33572/07_2026/7y1t_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7y1t_33572/07_2026/7y1t_33572.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y1t_33572/07_2026/7y1t_33572.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y1t_33572/07_2026/7y1t_33572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1t_33572/07_2026/7y1t_33572.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y1t_33572/07_2026/7y1t_33572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1t_33572/07_2026/7y1t_33572.map" } resolution = 3.24 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 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'GLU:plan': 8, 'ARG:plan': 9, 'ASN:plan1': 4, 'TYR:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1, 'TRP:plan': 1} 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 1.60, per 1000 atoms: 0.20 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: 0.74 Conformation dependent library (CDL) restraints added in 397.1 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: 0.18 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: 0.88 Time building geometry restraints manager: 0.86 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 - 17.95: 4350 17.95 - 35.89: 360 35.89 - 53.84: 53 53.84 - 71.78: 18 71.78 - 89.73: 7 Dihedral angle restraints: 4788 sinusoidal: 1837 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 4785 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: 3.680 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.860 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 8304 Z= 0.170 Angle : 0.884 30.865 11300 Z= 0.353 Chirality : 0.087 1.582 1292 Planarity : 0.004 0.104 1449 Dihedral : 13.774 89.727 2874 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG D 226 TYR 0.011 0.001 TYR A 200 PHE 0.017 0.001 PHE B 137 TRP 0.009 0.001 TRP A 179 HIS 0.002 0.000 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 ( 8278) covalent geometry : angle 0.58807 / 0.28 (11230) SS BOND : bond 0.00256 / 0.12 ( 8) SS BOND : angle 0.87807 / 0.51 ( 16) hydrogen bonds : bond 0.25773 / 16.37 ( 222) hydrogen bonds : angle 10.45088 / 7.12 ( 594) link_ALPHA1-3 : bond 0.00416 / 0.22 ( 1) link_ALPHA1-3 : angle 1.80026 / 1.39 ( 3) link_ALPHA1-4 : bond 0.01084 / 0.57 ( 1) link_ALPHA1-4 : angle 1.68503 / 1.30 ( 3) link_ALPHA1-6 : bond 0.00378 / 0.20 ( 1) link_ALPHA1-6 : angle 1.48862 / 1.26 ( 3) link_BETA1-4 : bond 0.01420 / 0.74 ( 6) link_BETA1-4 : angle 7.97537 / 6.07 ( 18) link_NAG-ASN : bond 0.03297 / 1.60 ( 9) link_NAG-ASN : angle 11.79741 / 7.13 ( 27) *********************** 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 : 0.305 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: 0.8080 (mt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0802 time to fit residues: 14.2266 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 : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3919 r_free = 0.3919 target = 0.130314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.102160 restraints weight = 14315.543| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.97 r_work: 0.3406 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8304 Z= 0.204 Angle : 0.682 9.191 11300 Z= 0.334 Chirality : 0.048 0.293 1292 Planarity : 0.005 0.079 1449 Dihedral : 4.093 21.053 1102 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.58 % Allowed : 10.83 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.27), residues: 1014 helix: 1.49 (0.54), residues: 105 sheet: -0.06 (0.27), residues: 374 loop : -1.27 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 215 TYR 0.015 0.002 TYR A 178 PHE 0.028 0.002 PHE B 137 TRP 0.011 0.001 TRP A 61 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 8278) covalent geometry : angle 0.66064 / 0.33 (11230) SS BOND : bond 0.00695 / 0.35 ( 8) SS BOND : angle 1.53368 / 0.89 ( 16) hydrogen bonds : bond 0.04172 / 2.73 ( 222) hydrogen bonds : angle 7.24680 / 4.95 ( 594) link_ALPHA1-3 : bond 0.00609 / 0.32 ( 1) link_ALPHA1-3 : angle 1.72544 / 1.10 ( 3) link_ALPHA1-4 : bond 0.01328 / 0.70 ( 1) link_ALPHA1-4 : angle 1.54709 / 1.25 ( 3) link_ALPHA1-6 : bond 0.00692 / 0.36 ( 1) link_ALPHA1-6 : angle 1.48191 / 1.38 ( 3) link_BETA1-4 : bond 0.00520 / 0.26 ( 6) link_BETA1-4 : angle 1.63095 / 0.95 ( 18) link_NAG-ASN : bond 0.00557 / 0.27 ( 9) link_NAG-ASN : angle 2.98356 / 1.95 ( 27) *********************** 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 102 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.6902 (p0) REVERT: A 474 PHE cc_start: 0.3600 (p90) cc_final: 0.3336 (p90) REVERT: B 141 ASP cc_start: 0.7618 (t0) cc_final: 0.6452 (p0) REVERT: B 224 CYS cc_start: 0.7664 (m) cc_final: 0.7438 (m) REVERT: B 374 MET cc_start: 0.6976 (tpt) cc_final: 0.6693 (tpt) REVERT: D 229 LEU cc_start: 0.8115 (mt) cc_final: 0.7903 (mt) outliers start: 13 outliers final: 11 residues processed: 98 average time/residue: 0.0789 time to fit residues: 11.2203 Evaluate side-chains 90 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 137 VAL 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 424 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 349 GLN 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 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3894 r_free = 0.3894 target = 0.128505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.100660 restraints weight = 14084.116| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.91 r_work: 0.3378 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8304 Z= 0.145 Angle : 0.622 16.561 11300 Z= 0.302 Chirality : 0.047 0.294 1292 Planarity : 0.004 0.061 1449 Dihedral : 3.999 19.598 1102 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.46 % Allowed : 13.87 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.26), residues: 1014 helix: 1.77 (0.57), residues: 96 sheet: -0.13 (0.27), residues: 368 loop : -1.15 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 215 TYR 0.013 0.001 TYR A 420 PHE 0.023 0.001 PHE B 137 TRP 0.009 0.001 TRP A 61 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 8278) covalent geometry : angle 0.60405 / 0.30 (11230) SS BOND : bond 0.00396 / 0.20 ( 8) SS BOND : angle 1.84322 / 1.08 ( 16) hydrogen bonds : bond 0.03357 / 2.17 ( 222) hydrogen bonds : angle 6.63246 / 4.55 ( 594) link_ALPHA1-3 : bond 0.00583 / 0.31 ( 1) link_ALPHA1-3 : angle 1.65092 / 1.07 ( 3) link_ALPHA1-4 : bond 0.01289 / 0.68 ( 1) link_ALPHA1-4 : angle 1.44145 / 1.22 ( 3) link_ALPHA1-6 : bond 0.00367 / 0.19 ( 1) link_ALPHA1-6 : angle 1.30371 / 1.08 ( 3) link_BETA1-4 : bond 0.00606 / 0.29 ( 6) link_BETA1-4 : angle 1.57003 / 0.92 ( 18) link_NAG-ASN : bond 0.00402 / 0.19 ( 9) link_NAG-ASN : angle 2.35111 / 1.54 ( 27) *********************** 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 92 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.221 Fit side-chains REVERT: A 108 CYS cc_start: 0.7083 (m) cc_final: 0.6625 (m) REVERT: A 474 PHE cc_start: 0.3231 (p90) cc_final: 0.2988 (p90) REVERT: B 141 ASP cc_start: 0.7707 (t0) cc_final: 0.6449 (p0) REVERT: B 224 CYS cc_start: 0.7636 (m) cc_final: 0.7434 (m) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.0824 time to fit residues: 10.0970 Evaluate side-chains 82 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 424 ILE Chi-restraints excluded: chain A residue 526 MET 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 59 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 100 optimal weight: 0.0370 chunk 52 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3856 r_free = 0.3856 target = 0.125814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.097713 restraints weight = 14316.359| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.92 r_work: 0.3328 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8304 Z= 0.152 Angle : 0.614 12.331 11300 Z= 0.300 Chirality : 0.046 0.275 1292 Planarity : 0.004 0.050 1449 Dihedral : 4.078 19.014 1102 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.68 % Allowed : 14.48 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.27), residues: 1014 helix: 1.52 (0.56), residues: 102 sheet: -0.24 (0.27), residues: 366 loop : -1.08 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 215 TYR 0.017 0.001 TYR A 420 PHE 0.022 0.001 PHE B 137 TRP 0.010 0.001 TRP A 61 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 8278) covalent geometry : angle 0.59514 / 0.29 (11230) SS BOND : bond 0.00594 / 0.31 ( 8) SS BOND : angle 2.38588 / 1.40 ( 16) hydrogen bonds : bond 0.03201 / 2.03 ( 222) hydrogen bonds : angle 6.11068 / 4.17 ( 594) link_ALPHA1-3 : bond 0.00457 / 0.24 ( 1) link_ALPHA1-3 : angle 1.50506 / 1.09 ( 3) link_ALPHA1-4 : bond 0.01192 / 0.63 ( 1) link_ALPHA1-4 : angle 1.43399 / 1.25 ( 3) link_ALPHA1-6 : bond 0.00596 / 0.31 ( 1) link_ALPHA1-6 : angle 1.40800 / 1.19 ( 3) link_BETA1-4 : bond 0.00505 / 0.24 ( 6) link_BETA1-4 : angle 1.59410 / 0.98 ( 18) link_NAG-ASN : bond 0.00372 / 0.18 ( 9) link_NAG-ASN : angle 2.12455 / 1.39 ( 27) *********************** 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 107 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.183 Fit side-chains REVERT: A 60 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7103 (p0) REVERT: A 368 ASP cc_start: 0.8220 (t0) cc_final: 0.7918 (t0) REVERT: A 474 PHE cc_start: 0.3123 (p90) cc_final: 0.2888 (p90) REVERT: B 323 GLU cc_start: 0.8502 (tt0) cc_final: 0.8019 (tp30) outliers start: 22 outliers final: 11 residues processed: 102 average time/residue: 0.0762 time to fit residues: 10.7746 Evaluate side-chains 87 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 97 SER 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 283 THR Chi-restraints excluded: chain A residue 424 ILE 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 65 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3843 r_free = 0.3843 target = 0.124877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097013 restraints weight = 14208.838| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.92 r_work: 0.3316 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8304 Z= 0.151 Angle : 0.611 14.061 11300 Z= 0.295 Chirality : 0.046 0.268 1292 Planarity : 0.004 0.047 1449 Dihedral : 4.069 18.162 1102 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.95 % Allowed : 17.03 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.27), residues: 1014 helix: 1.53 (0.56), residues: 102 sheet: -0.24 (0.27), residues: 373 loop : -1.08 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 226 TYR 0.012 0.001 TYR A 562 PHE 0.018 0.001 PHE B 137 TRP 0.012 0.001 TRP A 61 HIS 0.002 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 8278) covalent geometry : angle 0.59480 / 0.29 (11230) SS BOND : bond 0.00631 / 0.33 ( 8) SS BOND : angle 2.03702 / 1.22 ( 16) hydrogen bonds : bond 0.03018 / 1.95 ( 222) hydrogen bonds : angle 6.06111 / 4.12 ( 594) link_ALPHA1-3 : bond 0.00603 / 0.32 ( 1) link_ALPHA1-3 : angle 1.53093 / 1.14 ( 3) link_ALPHA1-4 : bond 0.01128 / 0.59 ( 1) link_ALPHA1-4 : angle 1.42732 / 1.25 ( 3) link_ALPHA1-6 : bond 0.00547 / 0.29 ( 1) link_ALPHA1-6 : angle 1.38840 / 1.18 ( 3) link_BETA1-4 : bond 0.00508 / 0.24 ( 6) link_BETA1-4 : angle 1.63717 / 1.00 ( 18) link_NAG-ASN : bond 0.00346 / 0.16 ( 9) link_NAG-ASN : angle 2.09757 / 1.37 ( 27) *********************** 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 92 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.223 Fit side-chains REVERT: A 60 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7213 (p0) REVERT: A 368 ASP cc_start: 0.8393 (t0) cc_final: 0.7944 (t0) REVERT: A 474 PHE cc_start: 0.3137 (p90) cc_final: 0.2880 (p90) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.0710 time to fit residues: 8.6514 Evaluate side-chains 86 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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 166 HIS 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 15 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 16 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3844 r_free = 0.3844 target = 0.124786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096747 restraints weight = 14260.218| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.93 r_work: 0.3313 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8304 Z= 0.143 Angle : 0.603 13.201 11300 Z= 0.292 Chirality : 0.046 0.259 1292 Planarity : 0.004 0.047 1449 Dihedral : 4.113 26.307 1102 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.80 % Allowed : 16.55 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.27), residues: 1014 helix: 1.56 (0.56), residues: 102 sheet: -0.26 (0.27), residues: 372 loop : -1.03 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 226 TYR 0.010 0.001 TYR A 562 PHE 0.030 0.001 PHE B 137 TRP 0.012 0.001 TRP A 61 HIS 0.002 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 8278) covalent geometry : angle 0.58633 / 0.29 (11230) SS BOND : bond 0.00806 / 0.41 ( 8) SS BOND : angle 2.13818 / 1.37 ( 16) hydrogen bonds : bond 0.02989 / 1.91 ( 222) hydrogen bonds : angle 5.96896 / 4.06 ( 594) link_ALPHA1-3 : bond 0.00604 / 0.32 ( 1) link_ALPHA1-3 : angle 1.51922 / 1.15 ( 3) link_ALPHA1-4 : bond 0.01144 / 0.60 ( 1) link_ALPHA1-4 : angle 1.43579 / 1.27 ( 3) link_ALPHA1-6 : bond 0.00549 / 0.29 ( 1) link_ALPHA1-6 : angle 1.38982 / 1.18 ( 3) link_BETA1-4 : bond 0.00497 / 0.24 ( 6) link_BETA1-4 : angle 1.65141 / 1.01 ( 18) link_NAG-ASN : bond 0.00323 / 0.15 ( 9) link_NAG-ASN : angle 2.04549 / 1.34 ( 27) *********************** 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 103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7223 (p0) REVERT: A 368 ASP cc_start: 0.8317 (t0) cc_final: 0.7933 (t0) REVERT: A 474 PHE cc_start: 0.3168 (p90) cc_final: 0.2927 (p90) REVERT: A 483 ASP cc_start: 0.7276 (t70) cc_final: 0.7019 (t70) REVERT: D 140 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5512 (tp30) outliers start: 23 outliers final: 14 residues processed: 95 average time/residue: 0.0798 time to fit residues: 10.8901 Evaluate side-chains 91 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 60 ASP 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 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 D residue 99 THR Chi-restraints excluded: chain D residue 140 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3845 r_free = 0.3845 target = 0.124934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096873 restraints weight = 14333.969| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.95 r_work: 0.3314 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8304 Z= 0.132 Angle : 0.595 12.469 11300 Z= 0.288 Chirality : 0.046 0.252 1292 Planarity : 0.004 0.049 1449 Dihedral : 4.070 25.979 1102 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.92 % Allowed : 16.91 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.27), residues: 1014 helix: 1.58 (0.56), residues: 102 sheet: -0.21 (0.27), residues: 372 loop : -1.02 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 215 TYR 0.010 0.001 TYR A 562 PHE 0.027 0.001 PHE B 137 TRP 0.011 0.001 TRP A 61 HIS 0.002 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 8278) covalent geometry : angle 0.57790 / 0.28 (11230) SS BOND : bond 0.00582 / 0.30 ( 8) SS BOND : angle 2.12065 / 1.40 ( 16) hydrogen bonds : bond 0.02951 / 1.88 ( 222) hydrogen bonds : angle 5.89747 / 4.01 ( 594) link_ALPHA1-3 : bond 0.00608 / 0.32 ( 1) link_ALPHA1-3 : angle 1.51757 / 1.16 ( 3) link_ALPHA1-4 : bond 0.01123 / 0.59 ( 1) link_ALPHA1-4 : angle 1.42961 / 1.26 ( 3) link_ALPHA1-6 : bond 0.00542 / 0.29 ( 1) link_ALPHA1-6 : angle 1.38613 / 1.18 ( 3) link_BETA1-4 : bond 0.00510 / 0.25 ( 6) link_BETA1-4 : angle 1.67036 / 1.03 ( 18) link_NAG-ASN : bond 0.00310 / 0.14 ( 9) link_NAG-ASN : angle 2.00270 / 1.31 ( 27) *********************** 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 102 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7132 (p0) REVERT: A 275 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.7392 (m-80) REVERT: A 368 ASP cc_start: 0.8316 (t0) cc_final: 0.7917 (t0) REVERT: A 474 PHE cc_start: 0.3122 (p90) cc_final: 0.2850 (p90) REVERT: A 483 ASP cc_start: 0.7352 (t70) cc_final: 0.7031 (t70) REVERT: A 497 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6694 (pp20) REVERT: D 140 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.5565 (tp30) outliers start: 24 outliers final: 16 residues processed: 95 average time/residue: 0.0757 time to fit residues: 10.3470 Evaluate side-chains 94 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 60 ASP 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 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 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 68 optimal weight: 0.7980 chunk 45 optimal weight: 0.0470 chunk 76 optimal weight: 0.9990 chunk 91 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3850 r_free = 0.3850 target = 0.125269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.097393 restraints weight = 14167.633| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.92 r_work: 0.3323 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8304 Z= 0.117 Angle : 0.583 11.543 11300 Z= 0.281 Chirality : 0.046 0.251 1292 Planarity : 0.004 0.050 1449 Dihedral : 4.017 25.441 1102 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.80 % Allowed : 17.27 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.27), residues: 1014 helix: 1.65 (0.56), residues: 102 sheet: -0.12 (0.27), residues: 361 loop : -1.03 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 215 TYR 0.009 0.001 TYR A 562 PHE 0.025 0.001 PHE B 137 TRP 0.009 0.001 TRP A 61 HIS 0.002 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8278) covalent geometry : angle 0.56706 / 0.28 (11230) SS BOND : bond 0.00541 / 0.28 ( 8) SS BOND : angle 1.96884 / 1.31 ( 16) hydrogen bonds : bond 0.02854 / 1.82 ( 222) hydrogen bonds : angle 5.81416 / 3.95 ( 594) link_ALPHA1-3 : bond 0.00615 / 0.32 ( 1) link_ALPHA1-3 : angle 1.52236 / 1.18 ( 3) link_ALPHA1-4 : bond 0.01153 / 0.61 ( 1) link_ALPHA1-4 : angle 1.43281 / 1.25 ( 3) link_ALPHA1-6 : bond 0.00535 / 0.28 ( 1) link_ALPHA1-6 : angle 1.38214 / 1.17 ( 3) link_BETA1-4 : bond 0.00534 / 0.26 ( 6) link_BETA1-4 : angle 1.67519 / 1.04 ( 18) link_NAG-ASN : bond 0.00302 / 0.14 ( 9) link_NAG-ASN : angle 1.94258 / 1.27 ( 27) *********************** 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 104 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7641 (t70) cc_final: 0.7128 (p0) REVERT: A 68 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: A 275 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: A 368 ASP cc_start: 0.8307 (t0) cc_final: 0.7893 (t0) REVERT: A 474 PHE cc_start: 0.3264 (p90) cc_final: 0.2991 (p90) REVERT: A 483 ASP cc_start: 0.7370 (t70) cc_final: 0.7062 (t70) REVERT: A 497 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6662 (pp20) REVERT: D 140 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5610 (tp30) outliers start: 23 outliers final: 16 residues processed: 96 average time/residue: 0.0746 time to fit residues: 10.2478 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 : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 68 GLN 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 243 VAL Chi-restraints excluded: chain A residue 275 TYR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3823 r_free = 0.3823 target = 0.123283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.095214 restraints weight = 14198.244| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.92 r_work: 0.3287 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8304 Z= 0.176 Angle : 0.618 11.370 11300 Z= 0.301 Chirality : 0.047 0.246 1292 Planarity : 0.004 0.051 1449 Dihedral : 4.160 27.043 1102 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.92 % Allowed : 17.52 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.27), residues: 1014 helix: 1.57 (0.56), residues: 102 sheet: -0.23 (0.27), residues: 372 loop : -1.03 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 214 TYR 0.012 0.001 TYR A 275 PHE 0.025 0.001 PHE B 137 TRP 0.010 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 8278) covalent geometry : angle 0.60112 / 0.30 (11230) SS BOND : bond 0.00560 / 0.29 ( 8) SS BOND : angle 2.06552 / 1.41 ( 16) hydrogen bonds : bond 0.03147 / 2.05 ( 222) hydrogen bonds : angle 5.89415 / 4.00 ( 594) link_ALPHA1-3 : bond 0.00579 / 0.30 ( 1) link_ALPHA1-3 : angle 1.47701 / 1.16 ( 3) link_ALPHA1-4 : bond 0.00935 / 0.49 ( 1) link_ALPHA1-4 : angle 1.45039 / 1.30 ( 3) link_ALPHA1-6 : bond 0.00588 / 0.31 ( 1) link_ALPHA1-6 : angle 1.38700 / 1.19 ( 3) link_BETA1-4 : bond 0.00531 / 0.25 ( 6) link_BETA1-4 : angle 1.68860 / 1.05 ( 18) link_NAG-ASN : bond 0.00306 / 0.14 ( 9) link_NAG-ASN : angle 2.05599 / 1.33 ( 27) *********************** 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 98 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: A 368 ASP cc_start: 0.8345 (t0) cc_final: 0.7981 (t0) REVERT: A 483 ASP cc_start: 0.7425 (t70) cc_final: 0.7169 (t70) REVERT: A 497 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6712 (pp20) REVERT: D 140 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5773 (tp30) outliers start: 24 outliers final: 18 residues processed: 92 average time/residue: 0.0696 time to fit residues: 9.2629 Evaluate side-chains 94 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP 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 212 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR 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 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 53 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3820 r_free = 0.3820 target = 0.122955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.095308 restraints weight = 14297.685| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.82 r_work: 0.3296 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8304 Z= 0.158 Angle : 0.612 10.940 11300 Z= 0.298 Chirality : 0.046 0.252 1292 Planarity : 0.004 0.051 1449 Dihedral : 4.178 27.300 1102 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.27), residues: 1014 helix: 1.45 (0.56), residues: 103 sheet: -0.14 (0.27), residues: 360 loop : -1.04 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 168 TYR 0.011 0.001 TYR A 178 PHE 0.025 0.001 PHE B 137 TRP 0.009 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 8278) covalent geometry : angle 0.59591 / 0.29 (11230) SS BOND : bond 0.00598 / 0.30 ( 8) SS BOND : angle 1.93064 / 1.29 ( 16) hydrogen bonds : bond 0.02999 / 1.95 ( 222) hydrogen bonds : angle 5.93602 / 4.04 ( 594) link_ALPHA1-3 : bond 0.00631 / 0.33 ( 1) link_ALPHA1-3 : angle 1.51152 / 1.21 ( 3) link_ALPHA1-4 : bond 0.01039 / 0.55 ( 1) link_ALPHA1-4 : angle 1.46595 / 1.32 ( 3) link_ALPHA1-6 : bond 0.00550 / 0.29 ( 1) link_ALPHA1-6 : angle 1.37926 / 1.17 ( 3) link_BETA1-4 : bond 0.00516 / 0.25 ( 6) link_BETA1-4 : angle 1.79957 / 1.13 ( 18) link_NAG-ASN : bond 0.00283 / 0.13 ( 9) link_NAG-ASN : angle 1.99356 / 1.30 ( 27) ********************** 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 97 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 225 SER cc_start: 0.8738 (t) cc_final: 0.8513 (p) REVERT: A 275 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: A 368 ASP cc_start: 0.8424 (t0) cc_final: 0.8089 (t0) REVERT: A 497 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6682 (pp20) REVERT: D 140 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5758 (tp30) REVERT: D 214 ARG cc_start: 0.7335 (mtm180) cc_final: 0.6349 (ptt180) outliers start: 21 outliers final: 18 residues processed: 93 average time/residue: 0.0777 time to fit residues: 10.0927 Evaluate side-chains 95 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR 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 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 80 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 78 optimal weight: 0.0070 chunk 6 optimal weight: 0.0040 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3821 r_free = 0.3821 target = 0.122919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.095442 restraints weight = 14281.152| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.80 r_work: 0.3295 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 8304 Z= 0.220 Angle : 0.978 59.104 11300 Z= 0.548 Chirality : 0.050 0.737 1292 Planarity : 0.004 0.051 1449 Dihedral : 4.175 27.252 1102 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.80 % Allowed : 17.52 % Favored : 79.68 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.27), residues: 1014 helix: 1.47 (0.56), residues: 103 sheet: -0.14 (0.27), residues: 360 loop : -1.04 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 398 TYR 0.010 0.001 TYR A 275 PHE 0.024 0.001 PHE B 137 TRP 0.010 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 ( 8278) covalent geometry : angle 0.96972 / 0.55 (11230) SS BOND : bond 0.00460 / 0.23 ( 8) SS BOND : angle 1.90694 / 1.25 ( 16) hydrogen bonds : bond 0.03015 / 1.95 ( 222) hydrogen bonds : angle 5.96720 / 4.07 ( 594) link_ALPHA1-3 : bond 0.00599 / 0.32 ( 1) link_ALPHA1-3 : angle 1.50738 / 1.20 ( 3) link_ALPHA1-4 : bond 0.01155 / 0.61 ( 1) link_ALPHA1-4 : angle 1.51026 / 1.37 ( 3) link_ALPHA1-6 : bond 0.00539 / 0.28 ( 1) link_ALPHA1-6 : angle 1.38559 / 1.18 ( 3) link_BETA1-4 : bond 0.00483 / 0.23 ( 6) link_BETA1-4 : angle 1.78878 / 1.13 ( 18) link_NAG-ASN : bond 0.00280 / 0.13 ( 9) link_NAG-ASN : angle 1.99098 / 1.29 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.80 seconds wall clock time: 29 minutes 55.06 seconds (1795.06 seconds total)