Starting phenix.real_space_refine on Fri Jul 3 23:01:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9j_44386/07_2026/9b9j_44386_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9j_44386/07_2026/9b9j_44386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b9j_44386/07_2026/9b9j_44386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9j_44386/07_2026/9b9j_44386.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9j_44386/07_2026/9b9j_44386_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9j_44386/07_2026/9b9j_44386_trim.cif" } resolution = 2.6 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= 0.038 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 7 9.91 5 S 36 5.16 5 C 5345 2.51 5 N 1367 2.21 5 O 1762 1.98 5 H 7817 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 16334 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 6568 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 32, 'TRANS': 417} Chain: "B" Number of atoms: 5900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5900 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 15, 'TRANS': 363} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1810 Classifications: {'peptide': 119} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "L" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1634 Classifications: {'peptide': 107} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "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: "I" 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: "J" 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: "K" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 14 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.62, per 1000 atoms: 0.16 Number of scatterers: 16334 At special positions: 0 Unit cell: (78.54, 106.59, 132.396, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 36 16.00 O 1762 8.00 N 1367 7.00 C 5345 6.00 H 7817 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 281 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 442 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 " " MAN G 4 " - " MAN G 5 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG B 804 " - " ASN B 397 " " NAG C 1 " - " ASN A 43 " " NAG D 1 " - " ASN A 141 " " NAG E 1 " - " ASN A 256 " " NAG F 1 " - " ASN A 266 " " NAG G 1 " - " ASN A 275 " " NAG I 1 " - " ASN B 192 " " NAG J 1 " - " ASN B 249 " " NAG K 1 " - " ASN B 343 " " NAG M 1 " - " ASN B 386 " " NAG N 1 " - " ASN H 60 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 362.6 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 20 sheets defined 14.8% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 80 through 86 removed outlier: 3.906A pdb=" N SER A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 144 through 154 removed outlier: 4.569A pdb=" N MET B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 208 through 218 removed outlier: 3.623A pdb=" N PHE B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 removed outlier: 4.287A pdb=" N ALA B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 245 Processing helix chain 'B' and resid 267 through 272 removed outlier: 4.319A pdb=" N GLY B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 321 through 332 removed outlier: 3.603A pdb=" N GLU B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'H' and resid 82C through 86 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.863A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.374A pdb=" N ARG A 423 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE A 434 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLY A 421 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY A 436 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 419 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 4.807A pdb=" N VAL A 55 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 108 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.642A pdb=" N SER A 169 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 238 removed outlier: 4.995A pdb=" N LYS A 254 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR A 259 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY A 260 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER A 277 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 262 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 292 removed outlier: 3.540A pdb=" N LEU A 340 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 312 Processing sheet with id=AA9, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 359 removed outlier: 6.364A pdb=" N LEU A 355 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLY A 372 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA A 370 " --> pdb=" O PRO A 357 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY A 359 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 400 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 71 removed outlier: 6.597A pdb=" N GLN B 98 " --> pdb=" O LYS B 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 109 through 116 removed outlier: 3.526A pdb=" N GLN B 405 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 199 through 206 removed outlier: 6.804A pdb=" N VAL B 202 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N SER B 166 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N SER B 204 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE B 164 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP B 124 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL B 255 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR B 126 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER B 257 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 128 " --> pdb=" O SER B 257 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.530A pdb=" N THR H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.530A pdb=" N THR H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.768A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.284A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.284A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 732 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: 2.78 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7817 1.03 - 1.23: 79 1.23 - 1.42: 3617 1.42 - 1.62: 4946 1.62 - 1.81: 54 Bond restraints: 16513 Sorted by residual: bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.98e+00 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C LYS A 125 " pdb=" N GLU A 126 " ideal model delta sigma weight residual 1.331 1.311 0.020 1.59e-02 3.96e+03 1.59e+00 bond pdb=" C5 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.413 1.438 -0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" C2 BMA G 3 " pdb=" C3 BMA G 3 " ideal model delta sigma weight residual 1.544 1.519 0.025 2.00e-02 2.50e+03 1.53e+00 ... (remaining 16508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 28481 1.37 - 2.74: 940 2.74 - 4.11: 110 4.11 - 5.49: 37 5.49 - 6.86: 15 Bond angle restraints: 29583 Sorted by residual: angle pdb=" CA SER A 63 " pdb=" C SER A 63 " pdb=" N PRO A 64 " ideal model delta sigma weight residual 118.44 122.90 -4.46 1.59e+00 3.96e-01 7.85e+00 angle pdb=" CA GLN H 83 " pdb=" CB GLN H 83 " pdb=" CG GLN H 83 " ideal model delta sigma weight residual 114.10 119.43 -5.33 2.00e+00 2.50e-01 7.10e+00 angle pdb=" CA GLU A 202 " pdb=" CB GLU A 202 " pdb=" CG GLU A 202 " ideal model delta sigma weight residual 114.10 119.20 -5.10 2.00e+00 2.50e-01 6.52e+00 angle pdb=" C SER A 63 " pdb=" CA SER A 63 " pdb=" CB SER A 63 " ideal model delta sigma weight residual 110.17 115.14 -4.97 1.97e+00 2.58e-01 6.36e+00 angle pdb=" CB GLU A 202 " pdb=" CG GLU A 202 " pdb=" CD GLU A 202 " ideal model delta sigma weight residual 112.60 116.77 -4.17 1.70e+00 3.46e-01 6.02e+00 ... (remaining 29578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 7735 23.28 - 46.56: 409 46.56 - 69.84: 105 69.84 - 93.13: 58 93.13 - 116.41: 45 Dihedral angle restraints: 8352 sinusoidal: 4824 harmonic: 3528 Sorted by residual: dihedral pdb=" CB CYS A 151 " pdb=" SG CYS A 151 " pdb=" SG CYS A 164 " pdb=" CB CYS A 164 " ideal model delta sinusoidal sigma weight residual 93.00 52.45 40.55 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" CA THR A 258 " pdb=" C THR A 258 " pdb=" N TYR A 259 " pdb=" CA TYR A 259 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA VAL B 172 " pdb=" C VAL B 172 " pdb=" N MET B 173 " pdb=" CA MET B 173 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 8349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1156 0.056 - 0.111: 166 0.111 - 0.166: 49 0.166 - 0.222: 1 0.222 - 0.277: 8 Chirality restraints: 1380 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1377 not shown) Planarity restraints: 2499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 415 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO B 416 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 416 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 416 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 83 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C GLN H 83 " -0.028 2.00e-02 2.50e+03 pdb=" O GLN H 83 " 0.010 2.00e-02 2.50e+03 pdb=" N SER H 84 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 182 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 183 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " 0.020 5.00e-02 4.00e+02 ... (remaining 2496 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 411 2.14 - 2.75: 29355 2.75 - 3.37: 44710 3.37 - 3.98: 60548 3.98 - 4.60: 94438 Nonbonded interactions: 229462 Sorted by model distance: nonbonded pdb=" OE1 GLU A 6 " pdb=" H GLU A 6 " model vdw 1.521 2.450 nonbonded pdb=" H LEU A 425 " pdb=" OD2 ASP A 432 " model vdw 1.556 2.450 nonbonded pdb=" O ASN A 2 " pdb=" H ARG A 449 " model vdw 1.637 2.450 nonbonded pdb=" OD1 ASN B 310 " pdb="HH12 ARG B 426 " model vdw 1.656 2.450 nonbonded pdb=" OE2 GLU A 94 " pdb=" HH TYR A 119 " model vdw 1.656 2.450 ... (remaining 229457 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 13.670 Find NCS groups from input model: 0.080 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:7.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.005 0.045 8737 Z= 0.232 Angle : 0.744 6.858 11914 Z= 0.357 Chirality : 0.049 0.277 1380 Planarity : 0.003 0.043 1496 Dihedral : 19.517 116.406 3667 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.04 % Rotamer: Outliers : 0.34 % Allowed : 5.49 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.15 (0.26), residues: 1047 helix: 0.16 (0.53), residues: 102 sheet: 0.71 (0.26), residues: 376 loop : -0.27 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.010 0.001 TYR B 325 PHE 0.012 0.001 PHE B 321 TRP 0.010 0.001 TRP A 121 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 ( 8696) covalent geometry : angle 0.72479 / 0.35 (11800) SS BOND : bond 0.00260 / 0.11 ( 9) SS BOND : angle 0.72920 / 0.41 ( 18) hydrogen bonds : bond 0.17353 / 11.48 ( 282) hydrogen bonds : angle 7.83758 / 5.43 ( 732) link_ALPHA1-3 : bond 0.00646 / 0.33 ( 3) link_ALPHA1-3 : angle 2.11901 / 1.41 ( 9) link_ALPHA1-6 : bond 0.00661 / 0.35 ( 1) link_ALPHA1-6 : angle 1.35880 / 1.10 ( 3) link_BETA1-4 : bond 0.00410 / 0.23 ( 17) link_BETA1-4 : angle 2.09237 / 1.30 ( 51) link_NAG-ASN : bond 0.00311 / 0.14 ( 11) link_NAG-ASN : angle 1.89909 / 1.20 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 PHE cc_start: 0.7449 (m-80) cc_final: 0.6805 (m-80) REVERT: A 220 ARG cc_start: 0.8739 (mtm180) cc_final: 0.8529 (mtm180) REVERT: A 335 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7733 (mp0) REVERT: B 69 ILE cc_start: 0.8072 (mt) cc_final: 0.7714 (mp) REVERT: B 73 LYS cc_start: 0.7123 (ttpt) cc_final: 0.6901 (ttpp) REVERT: B 95 GLN cc_start: 0.6769 (tt0) cc_final: 0.6335 (tp-100) REVERT: B 133 TYR cc_start: 0.8295 (t80) cc_final: 0.8064 (t80) REVERT: B 140 GLU cc_start: 0.8207 (tp30) cc_final: 0.7934 (mm-30) REVERT: B 402 ASP cc_start: 0.8041 (t0) cc_final: 0.7777 (t70) REVERT: H 100 MET cc_start: 0.8096 (tpt) cc_final: 0.7891 (tpt) REVERT: H 108 MET cc_start: 0.8144 (tmm) cc_final: 0.7904 (tmm) REVERT: L 45 LYS cc_start: 0.7668 (ttmm) cc_final: 0.7453 (tppt) REVERT: L 93 GLU cc_start: 0.8325 (pt0) cc_final: 0.8070 (pt0) REVERT: L 105 GLU cc_start: 0.4910 (OUTLIER) cc_final: 0.4564 (mt-10) outliers start: 3 outliers final: 1 residues processed: 124 average time/residue: 1.3561 time to fit residues: 177.4604 Evaluate side-chains 93 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 GLN B 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.096848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.067893 restraints weight = 34297.363| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.51 r_work: 0.2747 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8737 Z= 0.153 Angle : 0.656 6.971 11914 Z= 0.317 Chirality : 0.049 0.278 1380 Planarity : 0.004 0.051 1496 Dihedral : 14.518 107.842 1794 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 1.46 % Allowed : 9.19 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.15 (0.26), residues: 1047 helix: 0.13 (0.52), residues: 102 sheet: 0.72 (0.26), residues: 374 loop : -0.27 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 426 TYR 0.015 0.001 TYR A 261 PHE 0.011 0.001 PHE B 321 TRP 0.009 0.001 TRP A 121 HIS 0.006 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8696) covalent geometry : angle 0.63287 / 0.31 (11800) SS BOND : bond 0.00351 / 0.15 ( 9) SS BOND : angle 0.76524 / 0.44 ( 18) hydrogen bonds : bond 0.04314 / 2.87 ( 282) hydrogen bonds : angle 6.06122 / 4.12 ( 732) link_ALPHA1-3 : bond 0.00705 / 0.36 ( 3) link_ALPHA1-3 : angle 2.16675 / 1.39 ( 9) link_ALPHA1-6 : bond 0.00446 / 0.23 ( 1) link_ALPHA1-6 : angle 2.56062 / 1.41 ( 3) link_BETA1-4 : bond 0.00436 / 0.27 ( 17) link_BETA1-4 : angle 2.24083 / 1.44 ( 51) link_NAG-ASN : bond 0.00292 / 0.12 ( 11) link_NAG-ASN : angle 1.49905 / 0.94 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7484 (pm20) REVERT: A 71 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8443 (tt0) REVERT: A 155 PHE cc_start: 0.7840 (m-80) cc_final: 0.7235 (m-80) REVERT: A 335 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7732 (mp0) REVERT: A 363 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6546 (mp10) REVERT: B 69 ILE cc_start: 0.8178 (mt) cc_final: 0.7955 (mp) REVERT: B 150 MET cc_start: 0.8252 (mmt) cc_final: 0.7771 (mmt) REVERT: B 402 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7802 (t70) REVERT: H 100 MET cc_start: 0.8277 (tpt) cc_final: 0.8034 (tpt) REVERT: L 105 GLU cc_start: 0.4899 (tm-30) cc_final: 0.4538 (mt-10) outliers start: 13 outliers final: 5 residues processed: 92 average time/residue: 1.4270 time to fit residues: 138.5243 Evaluate side-chains 86 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain H residue 95 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.093820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.064838 restraints weight = 34963.289| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.50 r_work: 0.2712 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8737 Z= 0.169 Angle : 0.594 8.297 11914 Z= 0.295 Chirality : 0.046 0.305 1380 Planarity : 0.004 0.053 1496 Dihedral : 11.803 103.262 1791 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 1.23 % Allowed : 9.53 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.14 (0.26), residues: 1047 helix: 0.19 (0.51), residues: 103 sheet: 0.76 (0.26), residues: 375 loop : -0.33 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 76 TYR 0.013 0.002 TYR B 133 PHE 0.012 0.001 PHE B 321 TRP 0.013 0.002 TRP A 121 HIS 0.007 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 8696) covalent geometry : angle 0.57499 / 0.29 (11800) SS BOND : bond 0.00468 / 0.21 ( 9) SS BOND : angle 1.04199 / 0.64 ( 18) hydrogen bonds : bond 0.04507 / 2.97 ( 282) hydrogen bonds : angle 5.66095 / 3.87 ( 732) link_ALPHA1-3 : bond 0.00835 / 0.43 ( 3) link_ALPHA1-3 : angle 1.45318 / 0.98 ( 9) link_ALPHA1-6 : bond 0.00739 / 0.39 ( 1) link_ALPHA1-6 : angle 2.00108 / 1.16 ( 3) link_BETA1-4 : bond 0.00439 / 0.26 ( 17) link_BETA1-4 : angle 1.77896 / 1.14 ( 51) link_NAG-ASN : bond 0.00331 / 0.16 ( 11) link_NAG-ASN : angle 1.68194 / 1.09 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 PHE cc_start: 0.7873 (m-80) cc_final: 0.7314 (m-80) REVERT: A 335 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7759 (mp0) REVERT: A 363 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.6439 (mp10) REVERT: B 140 GLU cc_start: 0.8328 (tp30) cc_final: 0.8106 (mp0) REVERT: H 58 ASP cc_start: 0.8729 (m-30) cc_final: 0.8499 (t70) REVERT: H 86 ASP cc_start: 0.7963 (t0) cc_final: 0.7699 (t0) REVERT: H 100 MET cc_start: 0.8297 (tpt) cc_final: 0.8039 (tpt) REVERT: L 105 GLU cc_start: 0.4877 (tm-30) cc_final: 0.4465 (mm-30) outliers start: 11 outliers final: 5 residues processed: 83 average time/residue: 1.3565 time to fit residues: 119.0206 Evaluate side-chains 79 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 227 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.064301 restraints weight = 34878.600| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.49 r_work: 0.2695 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8737 Z= 0.173 Angle : 0.603 9.656 11914 Z= 0.297 Chirality : 0.047 0.297 1380 Planarity : 0.004 0.055 1496 Dihedral : 10.749 98.363 1791 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer: Outliers : 1.35 % Allowed : 9.98 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.09 (0.26), residues: 1047 helix: 0.06 (0.49), residues: 110 sheet: 0.76 (0.26), residues: 376 loop : -0.38 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 76 TYR 0.014 0.002 TYR B 133 PHE 0.013 0.001 PHE A 19 TRP 0.013 0.002 TRP A 121 HIS 0.007 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 ( 8696) covalent geometry : angle 0.58395 / 0.29 (11800) SS BOND : bond 0.00386 / 0.16 ( 9) SS BOND : angle 1.05722 / 0.63 ( 18) hydrogen bonds : bond 0.03834 / 2.54 ( 282) hydrogen bonds : angle 5.57237 / 3.79 ( 732) link_ALPHA1-3 : bond 0.00698 / 0.36 ( 3) link_ALPHA1-3 : angle 1.75452 / 1.14 ( 9) link_ALPHA1-6 : bond 0.00581 / 0.31 ( 1) link_ALPHA1-6 : angle 2.12269 / 1.22 ( 3) link_BETA1-4 : bond 0.00274 / 0.16 ( 17) link_BETA1-4 : angle 1.72664 / 1.11 ( 51) link_NAG-ASN : bond 0.00245 / 0.12 ( 11) link_NAG-ASN : angle 1.70814 / 1.16 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 363 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.6482 (mp10) REVERT: B 76 THR cc_start: 0.8242 (p) cc_final: 0.8013 (t) REVERT: B 140 GLU cc_start: 0.8314 (tp30) cc_final: 0.8068 (mp0) REVERT: B 402 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7862 (t0) REVERT: H 58 ASP cc_start: 0.8747 (m-30) cc_final: 0.8516 (t70) REVERT: H 86 ASP cc_start: 0.8063 (t0) cc_final: 0.7821 (t0) REVERT: L 105 GLU cc_start: 0.4929 (tm-30) cc_final: 0.4442 (mm-30) outliers start: 12 outliers final: 7 residues processed: 82 average time/residue: 1.2648 time to fit residues: 109.7601 Evaluate side-chains 80 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain H residue 95 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 ASN H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.092576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.063903 restraints weight = 34716.221| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.47 r_work: 0.2692 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8737 Z= 0.176 Angle : 0.601 11.062 11914 Z= 0.294 Chirality : 0.046 0.279 1380 Planarity : 0.004 0.056 1496 Dihedral : 9.769 93.020 1791 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer: Outliers : 1.57 % Allowed : 10.20 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.07 (0.26), residues: 1047 helix: 0.16 (0.50), residues: 110 sheet: 0.75 (0.26), residues: 376 loop : -0.43 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 76 TYR 0.013 0.002 TYR B 133 PHE 0.012 0.001 PHE A 19 TRP 0.013 0.002 TRP A 121 HIS 0.006 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 8696) covalent geometry : angle 0.58106 / 0.29 (11800) SS BOND : bond 0.00373 / 0.15 ( 9) SS BOND : angle 0.96874 / 0.56 ( 18) hydrogen bonds : bond 0.03873 / 2.57 ( 282) hydrogen bonds : angle 5.50805 / 3.75 ( 732) link_ALPHA1-3 : bond 0.00752 / 0.39 ( 3) link_ALPHA1-3 : angle 1.55837 / 1.01 ( 9) link_ALPHA1-6 : bond 0.00028 / 0.01 ( 1) link_ALPHA1-6 : angle 2.31398 / 1.37 ( 3) link_BETA1-4 : bond 0.00314 / 0.18 ( 17) link_BETA1-4 : angle 1.68920 / 1.09 ( 51) link_NAG-ASN : bond 0.00288 / 0.14 ( 11) link_NAG-ASN : angle 1.86285 / 1.37 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 363 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.6395 (mp10) REVERT: B 76 THR cc_start: 0.8385 (p) cc_final: 0.8164 (t) REVERT: B 140 GLU cc_start: 0.8282 (tp30) cc_final: 0.8027 (mp0) REVERT: H 58 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8488 (t70) REVERT: H 86 ASP cc_start: 0.8114 (t0) cc_final: 0.7881 (t0) REVERT: L 105 GLU cc_start: 0.4944 (tm-30) cc_final: 0.4387 (mm-30) outliers start: 14 outliers final: 7 residues processed: 79 average time/residue: 1.4701 time to fit residues: 122.4625 Evaluate side-chains 81 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 95 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 71 optimal weight: 0.0030 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 ASN H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.092972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.064273 restraints weight = 34743.266| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.47 r_work: 0.2695 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8737 Z= 0.156 Angle : 0.591 13.554 11914 Z= 0.287 Chirality : 0.044 0.273 1380 Planarity : 0.004 0.056 1496 Dihedral : 7.836 86.639 1791 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 1.57 % Allowed : 10.87 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.04 (0.26), residues: 1047 helix: 0.22 (0.50), residues: 110 sheet: 0.72 (0.26), residues: 378 loop : -0.46 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 155 TYR 0.012 0.001 TYR B 133 PHE 0.011 0.001 PHE B 321 TRP 0.011 0.002 TRP A 121 HIS 0.006 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 8696) covalent geometry : angle 0.55927 / 0.28 (11800) SS BOND : bond 0.00337 / 0.14 ( 9) SS BOND : angle 0.90701 / 0.53 ( 18) hydrogen bonds : bond 0.03600 / 2.39 ( 282) hydrogen bonds : angle 5.42350 / 3.69 ( 732) link_ALPHA1-3 : bond 0.00646 / 0.33 ( 3) link_ALPHA1-3 : angle 1.59365 / 1.06 ( 9) link_ALPHA1-6 : bond 0.00234 / 0.12 ( 1) link_ALPHA1-6 : angle 2.17898 / 1.37 ( 3) link_BETA1-4 : bond 0.00275 / 0.15 ( 17) link_BETA1-4 : angle 1.68402 / 1.10 ( 51) link_NAG-ASN : bond 0.00422 / 0.20 ( 11) link_NAG-ASN : angle 2.87307 / 2.58 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7719 (mm-30) REVERT: A 363 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6464 (mp10) REVERT: B 140 GLU cc_start: 0.8262 (tp30) cc_final: 0.8013 (mp0) REVERT: H 58 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8491 (t70) REVERT: H 86 ASP cc_start: 0.8127 (t0) cc_final: 0.7920 (t0) REVERT: L 105 GLU cc_start: 0.4957 (tm-30) cc_final: 0.4366 (mm-30) outliers start: 14 outliers final: 7 residues processed: 82 average time/residue: 1.3797 time to fit residues: 119.3332 Evaluate side-chains 81 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 95 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN B 383 ASN H 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.092513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.063758 restraints weight = 34652.222| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.47 r_work: 0.2685 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8737 Z= 0.178 Angle : 0.571 6.702 11914 Z= 0.286 Chirality : 0.044 0.221 1380 Planarity : 0.004 0.056 1496 Dihedral : 7.509 85.575 1791 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 1.79 % Allowed : 11.10 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.02 (0.26), residues: 1047 helix: 0.22 (0.50), residues: 110 sheet: 0.75 (0.27), residues: 376 loop : -0.50 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.013 0.002 TYR B 133 PHE 0.013 0.001 PHE A 19 TRP 0.013 0.002 TRP A 121 HIS 0.006 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 8696) covalent geometry : angle 0.55312 / 0.28 (11800) SS BOND : bond 0.00380 / 0.16 ( 9) SS BOND : angle 1.00217 / 0.58 ( 18) hydrogen bonds : bond 0.03762 / 2.50 ( 282) hydrogen bonds : angle 5.40868 / 3.69 ( 732) link_ALPHA1-3 : bond 0.00585 / 0.30 ( 3) link_ALPHA1-3 : angle 1.45544 / 0.98 ( 9) link_ALPHA1-6 : bond 0.00296 / 0.16 ( 1) link_ALPHA1-6 : angle 1.96141 / 1.36 ( 3) link_BETA1-4 : bond 0.00305 / 0.18 ( 17) link_BETA1-4 : angle 1.51295 / 0.99 ( 51) link_NAG-ASN : bond 0.00301 / 0.15 ( 11) link_NAG-ASN : angle 1.86254 / 1.36 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 363 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.6532 (mp10) REVERT: B 69 ILE cc_start: 0.8543 (mt) cc_final: 0.8341 (mp) REVERT: B 140 GLU cc_start: 0.8266 (tp30) cc_final: 0.8007 (mp0) REVERT: B 402 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7920 (t0) REVERT: H 58 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8485 (t70) REVERT: H 86 ASP cc_start: 0.8162 (t0) cc_final: 0.7944 (t0) REVERT: L 105 GLU cc_start: 0.4971 (tm-30) cc_final: 0.4356 (mm-30) outliers start: 16 outliers final: 10 residues processed: 84 average time/residue: 1.4185 time to fit residues: 125.5577 Evaluate side-chains 87 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain L residue 28 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 57 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 ASN H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.093782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.065378 restraints weight = 34608.316| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.45 r_work: 0.2707 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8737 Z= 0.126 Angle : 0.541 6.936 11914 Z= 0.270 Chirality : 0.043 0.242 1380 Planarity : 0.004 0.056 1496 Dihedral : 6.731 73.095 1791 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.94 % Rotamer: Outliers : 1.46 % Allowed : 11.55 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.08 (0.26), residues: 1047 helix: 0.36 (0.50), residues: 110 sheet: 0.75 (0.27), residues: 377 loop : -0.46 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 155 TYR 0.011 0.001 TYR B 133 PHE 0.011 0.001 PHE B 321 TRP 0.008 0.001 TRP A 121 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8696) covalent geometry : angle 0.52435 / 0.27 (11800) SS BOND : bond 0.00314 / 0.13 ( 9) SS BOND : angle 0.82391 / 0.47 ( 18) hydrogen bonds : bond 0.03344 / 2.22 ( 282) hydrogen bonds : angle 5.32545 / 3.62 ( 732) link_ALPHA1-3 : bond 0.00580 / 0.30 ( 3) link_ALPHA1-3 : angle 1.41918 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00015 / 0.01 ( 1) link_ALPHA1-6 : angle 1.85786 / 1.24 ( 3) link_BETA1-4 : bond 0.00290 / 0.16 ( 17) link_BETA1-4 : angle 1.49205 / 0.97 ( 51) link_NAG-ASN : bond 0.00210 / 0.10 ( 11) link_NAG-ASN : angle 1.66176 / 1.18 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8004 (mm-30) REVERT: A 363 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.6582 (mp10) REVERT: B 69 ILE cc_start: 0.8475 (mt) cc_final: 0.8271 (mp) REVERT: B 140 GLU cc_start: 0.8253 (tp30) cc_final: 0.7995 (mp0) REVERT: H 58 ASP cc_start: 0.8710 (m-30) cc_final: 0.8479 (t70) REVERT: H 75 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8060 (mm-40) REVERT: H 86 ASP cc_start: 0.8152 (t0) cc_final: 0.7947 (t0) REVERT: L 105 GLU cc_start: 0.4932 (tm-30) cc_final: 0.4285 (mm-30) outliers start: 13 outliers final: 11 residues processed: 85 average time/residue: 1.4342 time to fit residues: 128.3036 Evaluate side-chains 86 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain L residue 28 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 92 optimal weight: 0.0970 chunk 41 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 ASN H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.064664 restraints weight = 34767.129| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.44 r_work: 0.2689 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8737 Z= 0.157 Angle : 0.561 7.816 11914 Z= 0.279 Chirality : 0.044 0.242 1380 Planarity : 0.004 0.056 1496 Dihedral : 6.339 61.938 1791 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.94 % Rotamer: Outliers : 1.46 % Allowed : 11.88 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.04 (0.26), residues: 1047 helix: 0.36 (0.50), residues: 110 sheet: 0.72 (0.27), residues: 377 loop : -0.49 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 155 TYR 0.012 0.001 TYR B 133 PHE 0.011 0.001 PHE B 321 TRP 0.012 0.002 TRP A 121 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 8696) covalent geometry : angle 0.54269 / 0.28 (11800) SS BOND : bond 0.00356 / 0.15 ( 9) SS BOND : angle 0.98001 / 0.57 ( 18) hydrogen bonds : bond 0.03547 / 2.36 ( 282) hydrogen bonds : angle 5.31410 / 3.62 ( 732) link_ALPHA1-3 : bond 0.00568 / 0.29 ( 3) link_ALPHA1-3 : angle 1.45698 / 0.98 ( 9) link_ALPHA1-6 : bond 0.00123 / 0.06 ( 1) link_ALPHA1-6 : angle 1.84457 / 1.27 ( 3) link_BETA1-4 : bond 0.00293 / 0.16 ( 17) link_BETA1-4 : angle 1.56945 / 1.02 ( 51) link_NAG-ASN : bond 0.00273 / 0.13 ( 11) link_NAG-ASN : angle 1.71525 / 1.19 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7843 (mm-30) REVERT: A 363 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.6605 (mp10) REVERT: B 140 GLU cc_start: 0.8211 (tp30) cc_final: 0.7948 (mp0) REVERT: H 58 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8487 (t70) REVERT: H 75 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8060 (mm-40) REVERT: L 105 GLU cc_start: 0.5065 (tm-30) cc_final: 0.4362 (mm-30) outliers start: 13 outliers final: 10 residues processed: 78 average time/residue: 1.4260 time to fit residues: 117.0476 Evaluate side-chains 82 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 95 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 ASN H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.063545 restraints weight = 34842.041| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.48 r_work: 0.2687 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8737 Z= 0.184 Angle : 0.577 8.076 11914 Z= 0.287 Chirality : 0.044 0.231 1380 Planarity : 0.004 0.056 1496 Dihedral : 6.066 57.481 1791 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 1.35 % Allowed : 12.33 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -0.01 (0.26), residues: 1047 helix: 0.27 (0.50), residues: 110 sheet: 0.68 (0.27), residues: 379 loop : -0.51 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 155 TYR 0.014 0.002 TYR B 133 PHE 0.012 0.001 PHE A 19 TRP 0.013 0.002 TRP A 121 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 ( 8696) covalent geometry : angle 0.55800 / 0.28 (11800) SS BOND : bond 0.00370 / 0.15 ( 9) SS BOND : angle 1.04092 / 0.60 ( 18) hydrogen bonds : bond 0.03714 / 2.48 ( 282) hydrogen bonds : angle 5.37135 / 3.66 ( 732) link_ALPHA1-3 : bond 0.00563 / 0.29 ( 3) link_ALPHA1-3 : angle 1.43711 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00154 / 0.08 ( 1) link_ALPHA1-6 : angle 1.90011 / 1.26 ( 3) link_BETA1-4 : bond 0.00298 / 0.17 ( 17) link_BETA1-4 : angle 1.61934 / 1.05 ( 51) link_NAG-ASN : bond 0.00319 / 0.16 ( 11) link_NAG-ASN : angle 1.79389 / 1.22 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 363 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.6566 (mp10) REVERT: B 140 GLU cc_start: 0.8213 (tp30) cc_final: 0.7940 (mp0) REVERT: H 58 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8490 (t70) REVERT: H 75 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8069 (mm-40) REVERT: L 105 GLU cc_start: 0.5111 (tm-30) cc_final: 0.4371 (mm-30) outliers start: 12 outliers final: 10 residues processed: 80 average time/residue: 1.4974 time to fit residues: 126.1797 Evaluate side-chains 84 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 95 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 88 optimal weight: 0.0770 chunk 72 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 ASN H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.093200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.064621 restraints weight = 34776.002| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.48 r_work: 0.2707 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8737 Z= 0.132 Angle : 0.560 7.851 11914 Z= 0.277 Chirality : 0.043 0.200 1380 Planarity : 0.004 0.056 1496 Dihedral : 5.648 57.116 1791 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 1.35 % Allowed : 12.56 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.08 (0.26), residues: 1047 helix: 0.38 (0.50), residues: 110 sheet: 0.75 (0.27), residues: 377 loop : -0.46 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 155 TYR 0.012 0.001 TYR B 133 PHE 0.011 0.001 PHE B 321 TRP 0.009 0.001 TRP A 121 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 8696) covalent geometry : angle 0.54309 / 0.27 (11800) SS BOND : bond 0.00288 / 0.13 ( 9) SS BOND : angle 0.83951 / 0.48 ( 18) hydrogen bonds : bond 0.03375 / 2.24 ( 282) hydrogen bonds : angle 5.31296 / 3.61 ( 732) link_ALPHA1-3 : bond 0.00568 / 0.29 ( 3) link_ALPHA1-3 : angle 1.41356 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00063 / 0.03 ( 1) link_ALPHA1-6 : angle 1.76819 / 1.21 ( 3) link_BETA1-4 : bond 0.00291 / 0.16 ( 17) link_BETA1-4 : angle 1.57570 / 1.01 ( 51) link_NAG-ASN : bond 0.00201 / 0.09 ( 11) link_NAG-ASN : angle 1.60700 / 1.08 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5522.66 seconds wall clock time: 94 minutes 11.23 seconds (5651.23 seconds total)