Starting phenix.real_space_refine on Sun May 11 19:22:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1t_33572/05_2025/7y1t_33572.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1t_33572/05_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_33572/05_2025/7y1t_33572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1t_33572/05_2025/7y1t_33572.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1t_33572/05_2025/7y1t_33572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1t_33572/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.81, per 1000 atoms: 0.72 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: 2.46 Conformation dependent library (CDL) restraints added in 924.4 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: 0.96 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: 2.37 Time building geometry restraints manager: 2.71 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: 10.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.240 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.340 ------------------------------------------------------------------------------- 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 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 : 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 Details of bonding type rmsd link_NAG-ASN : bond 0.03297 ( 9) link_NAG-ASN : angle 11.79741 ( 27) link_ALPHA1-4 : bond 0.01084 ( 1) link_ALPHA1-4 : angle 1.68503 ( 3) link_ALPHA1-6 : bond 0.00378 ( 1) link_ALPHA1-6 : angle 1.48862 ( 3) link_BETA1-4 : bond 0.01420 ( 6) link_BETA1-4 : angle 7.97537 ( 18) link_ALPHA1-3 : bond 0.00416 ( 1) link_ALPHA1-3 : angle 1.80026 ( 3) hydrogen bonds : bond 0.25773 ( 222) hydrogen bonds : angle 10.45088 ( 594) SS BOND : bond 0.00256 ( 8) SS BOND : angle 0.87807 ( 16) covalent geometry : bond 0.00324 ( 8278) covalent geometry : angle 0.58807 (11230) *********************** 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 : 0.932 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: 0.2056 time to fit residues: 35.9081 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 : 0.972 ------------------------------------------------------------------------------- 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 = 0.132486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.104771 restraints weight = 14100.061| |-----------------------------------------------------------------------------| 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: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8304 Z= 0.176 Angle : 0.681 9.527 11300 Z= 0.325 Chirality : 0.048 0.276 1292 Planarity : 0.004 0.078 1449 Dihedral : 12.286 96.049 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 9) link_NAG-ASN : angle 2.61568 ( 27) link_ALPHA1-4 : bond 0.01458 ( 1) link_ALPHA1-4 : angle 1.11742 ( 3) link_ALPHA1-6 : bond 0.00414 ( 1) link_ALPHA1-6 : angle 1.45303 ( 3) link_BETA1-4 : bond 0.00595 ( 6) link_BETA1-4 : angle 1.98350 ( 18) link_ALPHA1-3 : bond 0.01459 ( 1) link_ALPHA1-3 : angle 2.21079 ( 3) hydrogen bonds : bond 0.03390 ( 222) hydrogen bonds : angle 7.12481 ( 594) SS BOND : bond 0.00592 ( 8) SS BOND : angle 1.44502 ( 16) covalent geometry : bond 0.00404 ( 8278) covalent geometry : angle 0.66273 (11230) *********************** 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: 10 poor density : 92 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7003 (p0) REVERT: A 474 PHE cc_start: 0.3558 (p90) cc_final: 0.3304 (p90) REVERT: B 224 CYS cc_start: 0.7722 (m) cc_final: 0.7480 (m) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.1916 time to fit residues: 26.3499 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 : 0.958 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.7980 chunk 56 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.128626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.100703 restraints weight = 14216.322| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.92 r_work: 0.3382 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8304 Z= 0.153 Angle : 0.644 14.465 11300 Z= 0.308 Chirality : 0.048 0.343 1292 Planarity : 0.004 0.057 1449 Dihedral : 10.457 94.221 1472 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.46 % Allowed : 13.38 % Favored : 85.16 % 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: -0.70 (0.27), residues: 1014 helix: 1.83 (0.58), residues: 96 sheet: -0.08 (0.27), residues: 374 loop : -1.17 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.003 0.001 HIS A 113 PHE 0.022 0.001 PHE B 137 TYR 0.013 0.001 TYR A 420 ARG 0.004 0.001 ARG D 215 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 9) link_NAG-ASN : angle 2.39305 ( 27) link_ALPHA1-4 : bond 0.01509 ( 1) link_ALPHA1-4 : angle 1.17103 ( 3) link_ALPHA1-6 : bond 0.00552 ( 1) link_ALPHA1-6 : angle 1.36150 ( 3) link_BETA1-4 : bond 0.00597 ( 6) link_BETA1-4 : angle 2.10941 ( 18) link_ALPHA1-3 : bond 0.01788 ( 1) link_ALPHA1-3 : angle 1.92190 ( 3) hydrogen bonds : bond 0.03449 ( 222) hydrogen bonds : angle 6.51868 ( 594) SS BOND : bond 0.00490 ( 8) SS BOND : angle 2.00016 ( 16) covalent geometry : bond 0.00352 ( 8278) covalent geometry : angle 0.62411 (11230) *********************** 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: 12 poor density : 83 time to evaluate : 0.961 Fit side-chains REVERT: A 108 CYS cc_start: 0.7078 (m) cc_final: 0.6626 (m) REVERT: A 474 PHE cc_start: 0.3621 (p90) cc_final: 0.3288 (p90) REVERT: B 141 ASP cc_start: 0.7709 (t0) cc_final: 0.6443 (p0) REVERT: B 224 CYS cc_start: 0.7670 (m) cc_final: 0.7465 (m) outliers start: 12 outliers final: 6 residues processed: 91 average time/residue: 0.2075 time to fit residues: 26.2825 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 : 0.958 ------------------------------------------------------------------------------- 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: 0.1980 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 93 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3882 r_free = 0.3882 target = 0.127693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.099931 restraints weight = 13981.649| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.90 r_work: 0.3370 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8304 Z= 0.136 Angle : 0.624 14.017 11300 Z= 0.298 Chirality : 0.046 0.300 1292 Planarity : 0.004 0.048 1449 Dihedral : 9.964 92.467 1472 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.82 % Allowed : 14.36 % Favored : 83.82 % 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: -0.70 (0.27), residues: 1014 helix: 1.91 (0.57), residues: 96 sheet: -0.18 (0.27), residues: 373 loop : -1.10 (0.27), residues: 545 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 0.019 0.001 PHE B 137 TYR 0.011 0.001 TYR A 562 ARG 0.004 0.000 ARG D 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 9) link_NAG-ASN : angle 2.22737 ( 27) link_ALPHA1-4 : bond 0.01485 ( 1) link_ALPHA1-4 : angle 1.11348 ( 3) link_ALPHA1-6 : bond 0.00512 ( 1) link_ALPHA1-6 : angle 1.41668 ( 3) link_BETA1-4 : bond 0.00532 ( 6) link_BETA1-4 : angle 2.14008 ( 18) link_ALPHA1-3 : bond 0.01581 ( 1) link_ALPHA1-3 : angle 1.43587 ( 3) hydrogen bonds : bond 0.03046 ( 222) hydrogen bonds : angle 6.18873 ( 594) SS BOND : bond 0.00566 ( 8) SS BOND : angle 2.15534 ( 16) covalent geometry : bond 0.00317 ( 8278) covalent geometry : angle 0.60350 (11230) *********************** 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 95 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.875 Fit side-chains REVERT: A 60 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7086 (p0) REVERT: A 368 ASP cc_start: 0.8101 (t0) cc_final: 0.7821 (t0) REVERT: A 474 PHE cc_start: 0.3289 (p90) cc_final: 0.3027 (p90) REVERT: B 141 ASP cc_start: 0.7688 (t0) cc_final: 0.6425 (p0) outliers start: 15 outliers final: 9 residues processed: 89 average time/residue: 0.1966 time to fit residues: 24.6020 Evaluate side-chains 86 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 299 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 45 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 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 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 = 0.3854 r_free = 0.3854 target = 0.125622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.097666 restraints weight = 13899.984| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.88 r_work: 0.3331 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8304 Z= 0.161 Angle : 0.637 13.442 11300 Z= 0.304 Chirality : 0.047 0.297 1292 Planarity : 0.004 0.046 1449 Dihedral : 9.668 90.911 1472 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.31 % Allowed : 15.69 % Favored : 82.00 % 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: 1.57 (0.56), residues: 102 sheet: -0.20 (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 B 307 PHE 0.019 0.001 PHE B 137 TYR 0.013 0.001 TYR A 420 ARG 0.003 0.000 ARG A 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 9) link_NAG-ASN : angle 2.25201 ( 27) link_ALPHA1-4 : bond 0.01482 ( 1) link_ALPHA1-4 : angle 1.12364 ( 3) link_ALPHA1-6 : bond 0.00513 ( 1) link_ALPHA1-6 : angle 1.41534 ( 3) link_BETA1-4 : bond 0.00520 ( 6) link_BETA1-4 : angle 2.24720 ( 18) link_ALPHA1-3 : bond 0.01490 ( 1) link_ALPHA1-3 : angle 1.21608 ( 3) hydrogen bonds : bond 0.03087 ( 222) hydrogen bonds : angle 6.06932 ( 594) SS BOND : bond 0.00557 ( 8) SS BOND : angle 2.18694 ( 16) covalent geometry : bond 0.00379 ( 8278) covalent geometry : angle 0.61664 (11230) *********************** 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: 19 poor density : 80 time to evaluate : 1.014 Fit side-chains REVERT: A 60 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7320 (p0) REVERT: A 368 ASP cc_start: 0.8194 (t0) cc_final: 0.7827 (t0) REVERT: A 474 PHE cc_start: 0.3125 (p90) cc_final: 0.2856 (p90) REVERT: B 141 ASP cc_start: 0.7651 (t0) cc_final: 0.6422 (p0) outliers start: 19 outliers final: 12 residues processed: 93 average time/residue: 0.1807 time to fit residues: 24.0144 Evaluate side-chains 88 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 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 189 THR 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: 1.9990 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 17 optimal weight: 0.0070 chunk 94 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.125563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.097467 restraints weight = 14114.428| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.91 r_work: 0.3324 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8304 Z= 0.144 Angle : 0.625 12.834 11300 Z= 0.298 Chirality : 0.047 0.292 1292 Planarity : 0.004 0.048 1449 Dihedral : 9.496 90.124 1472 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.19 % Allowed : 16.67 % 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: -0.72 (0.27), residues: 1014 helix: 1.58 (0.56), residues: 102 sheet: -0.24 (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 0.018 0.001 PHE B 137 TYR 0.010 0.001 TYR A 420 ARG 0.003 0.000 ARG A 398 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 9) link_NAG-ASN : angle 2.19057 ( 27) link_ALPHA1-4 : bond 0.01461 ( 1) link_ALPHA1-4 : angle 1.10353 ( 3) link_ALPHA1-6 : bond 0.00502 ( 1) link_ALPHA1-6 : angle 1.41822 ( 3) link_BETA1-4 : bond 0.00501 ( 6) link_BETA1-4 : angle 2.31816 ( 18) link_ALPHA1-3 : bond 0.01444 ( 1) link_ALPHA1-3 : angle 1.16585 ( 3) hydrogen bonds : bond 0.03014 ( 222) hydrogen bonds : angle 5.98017 ( 594) SS BOND : bond 0.00684 ( 8) SS BOND : angle 1.96937 ( 16) covalent geometry : bond 0.00338 ( 8278) covalent geometry : angle 0.60482 (11230) *********************** 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 95 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7206 (p0) REVERT: A 368 ASP cc_start: 0.8249 (t0) cc_final: 0.7848 (t0) REVERT: A 474 PHE cc_start: 0.3138 (p90) cc_final: 0.2890 (p90) REVERT: B 141 ASP cc_start: 0.7608 (t0) cc_final: 0.6364 (p0) outliers start: 18 outliers final: 11 residues processed: 89 average time/residue: 0.1966 time to fit residues: 25.0329 Evaluate side-chains 86 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 243 VAL Chi-restraints excluded: chain A residue 268 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.124885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.096944 restraints weight = 14125.075| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.86 r_work: 0.3316 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8304 Z= 0.150 Angle : 0.622 11.770 11300 Z= 0.298 Chirality : 0.047 0.288 1292 Planarity : 0.004 0.048 1449 Dihedral : 9.364 88.998 1472 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.55 % Allowed : 16.67 % Favored : 80.78 % 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: -0.67 (0.27), residues: 1014 helix: 1.61 (0.56), residues: 102 sheet: -0.13 (0.27), residues: 361 loop : -1.05 (0.27), residues: 551 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 0.029 0.001 PHE B 137 TYR 0.011 0.001 TYR A 562 ARG 0.003 0.000 ARG D 215 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 9) link_NAG-ASN : angle 2.17824 ( 27) link_ALPHA1-4 : bond 0.01443 ( 1) link_ALPHA1-4 : angle 1.10878 ( 3) link_ALPHA1-6 : bond 0.00501 ( 1) link_ALPHA1-6 : angle 1.41052 ( 3) link_BETA1-4 : bond 0.00502 ( 6) link_BETA1-4 : angle 2.35708 ( 18) link_ALPHA1-3 : bond 0.01394 ( 1) link_ALPHA1-3 : angle 1.14157 ( 3) hydrogen bonds : bond 0.03022 ( 222) hydrogen bonds : angle 5.94513 ( 594) SS BOND : bond 0.00772 ( 8) SS BOND : angle 1.97371 ( 16) covalent geometry : bond 0.00352 ( 8278) covalent geometry : angle 0.60213 (11230) *********************** 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 99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7210 (p0) REVERT: A 225 SER cc_start: 0.8715 (t) cc_final: 0.8449 (p) REVERT: A 275 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: A 368 ASP cc_start: 0.8279 (t0) cc_final: 0.7878 (t0) REVERT: A 474 PHE cc_start: 0.3204 (p90) cc_final: 0.2919 (p90) REVERT: A 483 ASP cc_start: 0.7285 (t70) cc_final: 0.7032 (t70) REVERT: B 141 ASP cc_start: 0.7657 (t0) cc_final: 0.6372 (p0) REVERT: D 140 GLU cc_start: 0.5992 (tp30) cc_final: 0.5587 (tp30) outliers start: 21 outliers final: 13 residues processed: 94 average time/residue: 0.1898 time to fit residues: 25.4191 Evaluate side-chains 93 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 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 D residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.124202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096496 restraints weight = 14274.773| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.80 r_work: 0.3310 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8304 Z= 0.156 Angle : 0.626 10.631 11300 Z= 0.301 Chirality : 0.047 0.288 1292 Planarity : 0.004 0.050 1449 Dihedral : 9.269 87.942 1472 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.80 % Allowed : 16.91 % Favored : 80.29 % 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: 1.56 (0.56), residues: 102 sheet: -0.13 (0.27), residues: 361 loop : -1.05 (0.27), residues: 551 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 0.027 0.001 PHE B 137 TYR 0.010 0.001 TYR A 562 ARG 0.002 0.000 ARG D 215 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 9) link_NAG-ASN : angle 2.17915 ( 27) link_ALPHA1-4 : bond 0.01366 ( 1) link_ALPHA1-4 : angle 1.10950 ( 3) link_ALPHA1-6 : bond 0.00445 ( 1) link_ALPHA1-6 : angle 1.38311 ( 3) link_BETA1-4 : bond 0.00474 ( 6) link_BETA1-4 : angle 2.41846 ( 18) link_ALPHA1-3 : bond 0.01336 ( 1) link_ALPHA1-3 : angle 1.11705 ( 3) hydrogen bonds : bond 0.03057 ( 222) hydrogen bonds : angle 5.93418 ( 594) SS BOND : bond 0.00621 ( 8) SS BOND : angle 1.87459 ( 16) covalent geometry : bond 0.00367 ( 8278) covalent geometry : angle 0.60566 (11230) *********************** 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 106 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7718 (t70) cc_final: 0.7140 (p0) REVERT: A 225 SER cc_start: 0.8744 (t) cc_final: 0.8487 (p) REVERT: A 275 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: A 368 ASP cc_start: 0.8280 (t0) cc_final: 0.7935 (t0) REVERT: A 409 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8660 (ptp) REVERT: A 474 PHE cc_start: 0.3293 (p90) cc_final: 0.3028 (p90) REVERT: A 483 ASP cc_start: 0.7362 (t70) cc_final: 0.7095 (t70) REVERT: B 141 ASP cc_start: 0.7686 (t0) cc_final: 0.6383 (p0) REVERT: D 140 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5562 (tp30) outliers start: 23 outliers final: 16 residues processed: 99 average time/residue: 0.1871 time to fit residues: 26.5021 Evaluate side-chains 98 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 0.0770 chunk 55 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.124017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.095931 restraints weight = 14479.730| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.95 r_work: 0.3296 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8304 Z= 0.150 Angle : 0.627 10.261 11300 Z= 0.301 Chirality : 0.047 0.287 1292 Planarity : 0.004 0.051 1449 Dihedral : 9.189 87.210 1472 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.68 % Allowed : 17.40 % 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 (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: 1.49 (0.56), residues: 103 sheet: -0.15 (0.27), residues: 361 loop : -1.03 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.027 0.001 PHE B 137 TYR 0.011 0.001 TYR A 562 ARG 0.002 0.000 ARG A 398 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 9) link_NAG-ASN : angle 2.16336 ( 27) link_ALPHA1-4 : bond 0.01356 ( 1) link_ALPHA1-4 : angle 1.10230 ( 3) link_ALPHA1-6 : bond 0.00506 ( 1) link_ALPHA1-6 : angle 1.39371 ( 3) link_BETA1-4 : bond 0.00493 ( 6) link_BETA1-4 : angle 2.46960 ( 18) link_ALPHA1-3 : bond 0.01325 ( 1) link_ALPHA1-3 : angle 1.11046 ( 3) hydrogen bonds : bond 0.03044 ( 222) hydrogen bonds : angle 5.91913 ( 594) SS BOND : bond 0.00679 ( 8) SS BOND : angle 1.81622 ( 16) covalent geometry : bond 0.00352 ( 8278) covalent geometry : angle 0.60677 (11230) *********************** 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 101 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 225 SER cc_start: 0.8780 (t) cc_final: 0.8515 (p) REVERT: A 275 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: A 368 ASP cc_start: 0.8436 (t0) cc_final: 0.7951 (t0) REVERT: A 409 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8680 (ptp) REVERT: A 483 ASP cc_start: 0.7407 (t70) cc_final: 0.7152 (t70) REVERT: B 141 ASP cc_start: 0.7713 (t0) cc_final: 0.6382 (p0) REVERT: D 140 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5625 (tp30) outliers start: 22 outliers final: 17 residues processed: 95 average time/residue: 0.1833 time to fit residues: 24.7176 Evaluate side-chains 96 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 137 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.123392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.095426 restraints weight = 14154.212| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.86 r_work: 0.3289 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8304 Z= 0.164 Angle : 0.636 10.303 11300 Z= 0.306 Chirality : 0.047 0.287 1292 Planarity : 0.004 0.052 1449 Dihedral : 9.150 86.480 1472 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.92 % Allowed : 17.40 % Favored : 79.68 % 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: -0.67 (0.27), residues: 1014 helix: 1.48 (0.56), residues: 103 sheet: -0.14 (0.27), residues: 361 loop : -1.02 (0.28), residues: 550 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 0.027 0.001 PHE B 137 TYR 0.011 0.001 TYR A 562 ARG 0.002 0.000 ARG D 215 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 9) link_NAG-ASN : angle 2.18351 ( 27) link_ALPHA1-4 : bond 0.01407 ( 1) link_ALPHA1-4 : angle 1.16500 ( 3) link_ALPHA1-6 : bond 0.00514 ( 1) link_ALPHA1-6 : angle 1.39738 ( 3) link_BETA1-4 : bond 0.00486 ( 6) link_BETA1-4 : angle 2.50841 ( 18) link_ALPHA1-3 : bond 0.01283 ( 1) link_ALPHA1-3 : angle 1.09504 ( 3) hydrogen bonds : bond 0.03126 ( 222) hydrogen bonds : angle 5.94892 ( 594) SS BOND : bond 0.00680 ( 8) SS BOND : angle 1.82377 ( 16) covalent geometry : bond 0.00388 ( 8278) covalent geometry : angle 0.61563 (11230) ********************** 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 102 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 225 SER cc_start: 0.8798 (t) cc_final: 0.8525 (p) REVERT: A 275 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: A 368 ASP cc_start: 0.8385 (t0) cc_final: 0.7971 (t0) REVERT: A 409 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8661 (ptp) REVERT: A 483 ASP cc_start: 0.7500 (t70) cc_final: 0.7190 (t70) REVERT: B 141 ASP cc_start: 0.7678 (t0) cc_final: 0.6299 (p0) REVERT: D 140 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5598 (tp30) outliers start: 24 outliers final: 20 residues processed: 97 average time/residue: 0.1880 time to fit residues: 25.8954 Evaluate side-chains 99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 137 VAL 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 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 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 63 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 98 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3840 r_free = 0.3840 target = 0.124559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.096564 restraints weight = 14205.388| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.93 r_work: 0.3306 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8304 Z= 0.118 Angle : 0.611 10.428 11300 Z= 0.292 Chirality : 0.046 0.283 1292 Planarity : 0.004 0.052 1449 Dihedral : 9.024 85.927 1472 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.68 % Allowed : 17.64 % Favored : 79.68 % 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: -0.67 (0.27), residues: 1014 helix: 1.55 (0.56), residues: 103 sheet: -0.17 (0.27), residues: 361 loop : -1.00 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 9) link_NAG-ASN : angle 2.08288 ( 27) link_ALPHA1-4 : bond 0.01340 ( 1) link_ALPHA1-4 : angle 1.05283 ( 3) link_ALPHA1-6 : bond 0.00492 ( 1) link_ALPHA1-6 : angle 1.40110 ( 3) link_BETA1-4 : bond 0.00503 ( 6) link_BETA1-4 : angle 2.53271 ( 18) link_ALPHA1-3 : bond 0.01275 ( 1) link_ALPHA1-3 : angle 1.13541 ( 3) hydrogen bonds : bond 0.02882 ( 222) hydrogen bonds : angle 5.86556 ( 594) SS BOND : bond 0.00581 ( 8) SS BOND : angle 1.61331 ( 16) covalent geometry : bond 0.00272 ( 8278) covalent geometry : angle 0.59119 (11230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3916.19 seconds wall clock time: 68 minutes 57.01 seconds (4137.01 seconds total)