Starting phenix.real_space_refine on Sun May 18 08:48:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9j_44386/05_2025/9b9j_44386_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9j_44386/05_2025/9b9j_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_44386/05_2025/9b9j_44386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9j_44386/05_2025/9b9j_44386.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9j_44386/05_2025/9b9j_44386_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9j_44386/05_2025/9b9j_44386_trim.cif" } resolution = 2.6 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= 0.038 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 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: 8.75, per 1000 atoms: 0.54 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: 5.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.59 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: 6.10 Time building geometry restraints manager: 6.01 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: 2.290 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: 0.290 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.290 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 (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: 0.15 (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 TRP 0.010 0.001 TRP A 121 HIS 0.004 0.001 HIS L 91 PHE 0.012 0.001 PHE B 321 TYR 0.010 0.001 TYR B 325 ARG 0.002 0.000 ARG B 155 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 11) link_NAG-ASN : angle 1.89909 ( 33) link_ALPHA1-6 : bond 0.00661 ( 1) link_ALPHA1-6 : angle 1.35880 ( 3) link_BETA1-4 : bond 0.00410 ( 17) link_BETA1-4 : angle 2.09237 ( 51) link_ALPHA1-3 : bond 0.00646 ( 3) link_ALPHA1-3 : angle 2.11901 ( 9) hydrogen bonds : bond 0.17353 ( 282) hydrogen bonds : angle 7.83758 ( 732) SS BOND : bond 0.00260 ( 9) SS BOND : angle 0.72920 ( 18) covalent geometry : bond 0.00499 ( 8696) covalent geometry : angle 0.72479 (11800) *********************** 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 : 1.246 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: 0.7722 (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: 0.7892 (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: 3.0064 time to fit residues: 393.2775 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 : 1.372 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3229 r_free = 0.3229 target = 0.096038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.067204 restraints weight = 34507.871| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.50 r_work: 0.2733 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1526 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= 0.148 Angle : 0.648 7.158 11914 Z= 0.311 Chirality : 0.049 0.273 1380 Planarity : 0.004 0.052 1496 Dihedral : 14.550 107.363 1794 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 1.46 % Allowed : 9.42 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.17 (0.26), residues: 1047 helix: 0.13 (0.52), residues: 102 sheet: 0.70 (0.26), residues: 372 loop : -0.23 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 121 HIS 0.007 0.001 HIS L 91 PHE 0.012 0.001 PHE A 19 TYR 0.015 0.001 TYR A 261 ARG 0.005 0.001 ARG B 426 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 11) link_NAG-ASN : angle 1.54057 ( 33) link_ALPHA1-6 : bond 0.00459 ( 1) link_ALPHA1-6 : angle 2.66669 ( 3) link_BETA1-4 : bond 0.00398 ( 17) link_BETA1-4 : angle 2.23194 ( 51) link_ALPHA1-3 : bond 0.00793 ( 3) link_ALPHA1-3 : angle 2.46128 ( 9) hydrogen bonds : bond 0.04522 ( 282) hydrogen bonds : angle 6.06296 ( 732) SS BOND : bond 0.00360 ( 9) SS BOND : angle 0.72679 ( 18) covalent geometry : bond 0.00343 ( 8696) covalent geometry : angle 0.62319 (11800) *********************** 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 : 1.252 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7466 (pm20) REVERT: A 71 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8443 (tt0) REVERT: A 155 PHE cc_start: 0.7807 (m-80) cc_final: 0.7198 (m-80) REVERT: A 335 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7705 (mp0) REVERT: A 363 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6336 (mp10) REVERT: B 69 ILE cc_start: 0.8143 (mt) cc_final: 0.7900 (mp) REVERT: B 150 MET cc_start: 0.8227 (mmt) cc_final: 0.7745 (mmt) REVERT: B 402 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7782 (t70) REVERT: H 100 MET cc_start: 0.8271 (tpt) cc_final: 0.8020 (tpt) REVERT: L 17 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7919 (mt-10) REVERT: L 105 GLU cc_start: 0.4941 (tm-30) cc_final: 0.4506 (mt-10) outliers start: 13 outliers final: 4 residues processed: 92 average time/residue: 3.1466 time to fit residues: 305.1857 Evaluate side-chains 86 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.064669 restraints weight = 34654.907| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.46 r_work: 0.2703 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2535 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= 0.170 Angle : 0.597 8.675 11914 Z= 0.296 Chirality : 0.046 0.298 1380 Planarity : 0.004 0.053 1496 Dihedral : 11.648 102.172 1791 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.48 % Favored : 97.42 % Rotamer: Outliers : 1.79 % Allowed : 9.64 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1047 helix: 0.20 (0.51), residues: 103 sheet: 0.76 (0.26), residues: 376 loop : -0.30 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 121 HIS 0.007 0.001 HIS L 91 PHE 0.012 0.001 PHE B 321 TYR 0.013 0.002 TYR B 133 ARG 0.003 0.000 ARG B 393 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 11) link_NAG-ASN : angle 1.71697 ( 33) link_ALPHA1-6 : bond 0.00614 ( 1) link_ALPHA1-6 : angle 1.91904 ( 3) link_BETA1-4 : bond 0.00463 ( 17) link_BETA1-4 : angle 1.62839 ( 51) link_ALPHA1-3 : bond 0.00862 ( 3) link_ALPHA1-3 : angle 1.40679 ( 9) hydrogen bonds : bond 0.04525 ( 282) hydrogen bonds : angle 5.60699 ( 732) SS BOND : bond 0.00394 ( 9) SS BOND : angle 1.01445 ( 18) covalent geometry : bond 0.00403 ( 8696) covalent geometry : angle 0.58013 (11800) *********************** 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 96 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.6432 (mp10) REVERT: B 140 GLU cc_start: 0.8323 (tp30) cc_final: 0.8119 (mp0) REVERT: B 236 MET cc_start: 0.8930 (tpp) cc_final: 0.8714 (tpp) REVERT: H 58 ASP cc_start: 0.8717 (m-30) cc_final: 0.8503 (t70) REVERT: L 17 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7786 (mt-10) REVERT: L 105 GLU cc_start: 0.4750 (tm-30) cc_final: 0.4386 (mm-30) outliers start: 16 outliers final: 7 residues processed: 89 average time/residue: 3.0274 time to fit residues: 284.5854 Evaluate side-chains 80 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain H residue 95 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.093788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.065376 restraints weight = 34570.512| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.44 r_work: 0.2717 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2763 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= 0.120 Angle : 0.570 9.785 11914 Z= 0.278 Chirality : 0.045 0.284 1380 Planarity : 0.004 0.056 1496 Dihedral : 10.521 98.077 1791 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.23 % Rotamer: Outliers : 1.23 % Allowed : 10.31 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.17 (0.26), residues: 1047 helix: 0.15 (0.49), residues: 110 sheet: 0.75 (0.27), residues: 376 loop : -0.28 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 121 HIS 0.005 0.001 HIS L 91 PHE 0.011 0.001 PHE B 321 TYR 0.013 0.001 TYR A 261 ARG 0.003 0.000 ARG L 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 11) link_NAG-ASN : angle 1.56666 ( 33) link_ALPHA1-6 : bond 0.00698 ( 1) link_ALPHA1-6 : angle 1.99208 ( 3) link_BETA1-4 : bond 0.00312 ( 17) link_BETA1-4 : angle 1.67849 ( 51) link_ALPHA1-3 : bond 0.00690 ( 3) link_ALPHA1-3 : angle 1.65384 ( 9) hydrogen bonds : bond 0.03419 ( 282) hydrogen bonds : angle 5.46168 ( 732) SS BOND : bond 0.00326 ( 9) SS BOND : angle 0.83246 ( 18) covalent geometry : bond 0.00286 ( 8696) covalent geometry : angle 0.55257 (11800) *********************** 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: 11 poor density : 76 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 363 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.6494 (mp10) REVERT: B 76 THR cc_start: 0.8176 (p) cc_final: 0.7951 (t) REVERT: B 140 GLU cc_start: 0.8314 (tp30) cc_final: 0.8082 (mp0) REVERT: B 402 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7781 (t0) REVERT: H 58 ASP cc_start: 0.8702 (m-30) cc_final: 0.8501 (t70) REVERT: L 17 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7796 (mt-10) REVERT: L 105 GLU cc_start: 0.4914 (tm-30) cc_final: 0.4435 (mm-30) outliers start: 11 outliers final: 6 residues processed: 82 average time/residue: 3.2916 time to fit residues: 283.6483 Evaluate side-chains 81 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 113 LEU 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 30 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.063566 restraints weight = 35237.188| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.46 r_work: 0.2676 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8737 Z= 0.192 Angle : 0.607 10.962 11914 Z= 0.296 Chirality : 0.046 0.280 1380 Planarity : 0.004 0.056 1496 Dihedral : 9.600 93.791 1791 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.47 % Rotamer: Outliers : 1.01 % Allowed : 10.43 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1047 helix: 0.19 (0.50), residues: 110 sheet: 0.72 (0.26), residues: 378 loop : -0.33 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 121 HIS 0.006 0.001 HIS L 91 PHE 0.014 0.002 PHE A 19 TYR 0.013 0.002 TYR B 133 ARG 0.002 0.000 ARG B 155 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 11) link_NAG-ASN : angle 1.90027 ( 33) link_ALPHA1-6 : bond 0.00194 ( 1) link_ALPHA1-6 : angle 2.83175 ( 3) link_BETA1-4 : bond 0.00311 ( 17) link_BETA1-4 : angle 1.73174 ( 51) link_ALPHA1-3 : bond 0.00629 ( 3) link_ALPHA1-3 : angle 1.60912 ( 9) hydrogen bonds : bond 0.03914 ( 282) hydrogen bonds : angle 5.50289 ( 732) SS BOND : bond 0.00389 ( 9) SS BOND : angle 1.04564 ( 18) covalent geometry : bond 0.00466 ( 8696) covalent geometry : angle 0.58603 (11800) *********************** 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 82 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 363 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.6512 (mp10) REVERT: B 68 ASP cc_start: 0.7524 (p0) cc_final: 0.7306 (p0) REVERT: B 76 THR cc_start: 0.8209 (p) cc_final: 0.7998 (t) REVERT: B 140 GLU cc_start: 0.8298 (tp30) cc_final: 0.8049 (mp0) REVERT: B 402 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7834 (t0) REVERT: H 58 ASP cc_start: 0.8725 (m-30) cc_final: 0.8485 (t70) REVERT: L 17 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7776 (mt-10) REVERT: L 105 GLU cc_start: 0.4918 (tm-30) cc_final: 0.4429 (mm-30) outliers start: 9 outliers final: 4 residues processed: 79 average time/residue: 3.2494 time to fit residues: 270.4084 Evaluate side-chains 77 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain B residue 402 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 101 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 81 optimal weight: 0.0470 chunk 99 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3182 r_free = 0.3182 target = 0.093095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.064687 restraints weight = 34845.395| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.45 r_work: 0.2697 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3085 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= 0.129 Angle : 0.575 12.412 11914 Z= 0.277 Chirality : 0.044 0.266 1380 Planarity : 0.004 0.056 1496 Dihedral : 7.948 87.552 1791 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 1.01 % Allowed : 10.87 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.15 (0.26), residues: 1047 helix: 0.36 (0.50), residues: 110 sheet: 0.71 (0.27), residues: 379 loop : -0.32 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 121 HIS 0.006 0.001 HIS L 91 PHE 0.011 0.001 PHE B 321 TYR 0.012 0.001 TYR A 261 ARG 0.002 0.000 ARG L 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 11) link_NAG-ASN : angle 2.65009 ( 33) link_ALPHA1-6 : bond 0.00203 ( 1) link_ALPHA1-6 : angle 2.10036 ( 3) link_BETA1-4 : bond 0.00283 ( 17) link_BETA1-4 : angle 1.64583 ( 51) link_ALPHA1-3 : bond 0.00714 ( 3) link_ALPHA1-3 : angle 1.48136 ( 9) hydrogen bonds : bond 0.03365 ( 282) hydrogen bonds : angle 5.36378 ( 732) SS BOND : bond 0.00320 ( 9) SS BOND : angle 0.81520 ( 18) covalent geometry : bond 0.00314 ( 8696) covalent geometry : angle 0.54627 (11800) *********************** 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 84 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 363 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.6530 (mp10) REVERT: B 68 ASP cc_start: 0.7346 (p0) cc_final: 0.7127 (p0) REVERT: B 76 THR cc_start: 0.8332 (p) cc_final: 0.8120 (t) REVERT: B 140 GLU cc_start: 0.8260 (tp30) cc_final: 0.8021 (mp0) REVERT: B 402 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7972 (t0) REVERT: H 58 ASP cc_start: 0.8723 (m-30) cc_final: 0.8496 (t70) REVERT: L 17 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7766 (mt-10) REVERT: L 105 GLU cc_start: 0.4811 (tm-30) cc_final: 0.4296 (mm-30) outliers start: 9 outliers final: 4 residues processed: 80 average time/residue: 3.2126 time to fit residues: 270.7400 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 : 1.228 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain B residue 402 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 81 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3175 r_free = 0.3175 target = 0.092703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.064246 restraints weight = 34875.985| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.45 r_work: 0.2686 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3200 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= 0.151 Angle : 0.552 6.766 11914 Z= 0.275 Chirality : 0.044 0.224 1380 Planarity : 0.004 0.056 1496 Dihedral : 7.391 85.968 1791 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer: Outliers : 1.23 % Allowed : 11.55 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.17 (0.26), residues: 1047 helix: 0.39 (0.50), residues: 110 sheet: 0.73 (0.27), residues: 378 loop : -0.33 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 121 HIS 0.006 0.001 HIS L 91 PHE 0.011 0.001 PHE B 321 TYR 0.012 0.001 TYR B 133 ARG 0.003 0.000 ARG B 155 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 11) link_NAG-ASN : angle 1.91457 ( 33) link_ALPHA1-6 : bond 0.00170 ( 1) link_ALPHA1-6 : angle 1.96442 ( 3) link_BETA1-4 : bond 0.00300 ( 17) link_BETA1-4 : angle 1.49343 ( 51) link_ALPHA1-3 : bond 0.00605 ( 3) link_ALPHA1-3 : angle 1.48543 ( 9) hydrogen bonds : bond 0.03530 ( 282) hydrogen bonds : angle 5.34356 ( 732) SS BOND : bond 0.00341 ( 9) SS BOND : angle 0.92521 ( 18) covalent geometry : bond 0.00368 ( 8696) covalent geometry : angle 0.53242 (11800) *********************** 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 86 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7757 (mm-30) REVERT: A 363 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.6602 (mp10) REVERT: B 68 ASP cc_start: 0.7377 (p0) cc_final: 0.7136 (p0) REVERT: B 140 GLU cc_start: 0.8274 (tp30) cc_final: 0.8028 (mp0) REVERT: B 402 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7939 (t0) REVERT: H 58 ASP cc_start: 0.8730 (m-30) cc_final: 0.8490 (t70) REVERT: H 83 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8256 (tm-30) REVERT: L 17 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7751 (mt-10) REVERT: L 105 GLU cc_start: 0.4822 (tm-30) cc_final: 0.4292 (mm-30) outliers start: 11 outliers final: 6 residues processed: 81 average time/residue: 3.1966 time to fit residues: 272.7861 Evaluate side-chains 81 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 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 L residue 28 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3176 r_free = 0.3176 target = 0.092769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.064354 restraints weight = 34648.055| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.45 r_work: 0.2692 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3287 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= 0.141 Angle : 0.547 6.999 11914 Z= 0.273 Chirality : 0.044 0.242 1380 Planarity : 0.004 0.056 1496 Dihedral : 6.747 73.517 1791 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 1.46 % Allowed : 11.43 % 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 (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: 0.19 (0.26), residues: 1047 helix: 0.44 (0.50), residues: 110 sheet: 0.75 (0.27), residues: 377 loop : -0.33 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 121 HIS 0.005 0.001 HIS L 91 PHE 0.011 0.001 PHE B 321 TYR 0.011 0.001 TYR B 133 ARG 0.004 0.000 ARG B 155 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 11) link_NAG-ASN : angle 1.74200 ( 33) link_ALPHA1-6 : bond 0.00082 ( 1) link_ALPHA1-6 : angle 1.85061 ( 3) link_BETA1-4 : bond 0.00288 ( 17) link_BETA1-4 : angle 1.52259 ( 51) link_ALPHA1-3 : bond 0.00599 ( 3) link_ALPHA1-3 : angle 1.43319 ( 9) hydrogen bonds : bond 0.03422 ( 282) hydrogen bonds : angle 5.31564 ( 732) SS BOND : bond 0.00319 ( 9) SS BOND : angle 0.89342 ( 18) covalent geometry : bond 0.00340 ( 8696) covalent geometry : angle 0.52953 (11800) *********************** 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 89 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 363 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.6610 (mp10) REVERT: B 68 ASP cc_start: 0.7386 (p0) cc_final: 0.7112 (p0) REVERT: B 69 ILE cc_start: 0.8416 (mp) cc_final: 0.8211 (mp) REVERT: B 140 GLU cc_start: 0.8260 (tp30) cc_final: 0.8007 (mp0) REVERT: B 402 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7913 (t0) REVERT: H 58 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8492 (t70) REVERT: H 75 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8034 (mm-40) REVERT: H 83 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8249 (tm-30) REVERT: L 17 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7730 (mt-10) REVERT: L 105 GLU cc_start: 0.4883 (tm-30) cc_final: 0.4337 (mm-30) outliers start: 13 outliers final: 7 residues processed: 82 average time/residue: 3.2057 time to fit residues: 277.1009 Evaluate side-chains 84 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 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 B residue 402 ASP Chi-restraints excluded: chain H residue 58 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 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3193 r_free = 0.3193 target = 0.093862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.065382 restraints weight = 34785.244| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.48 r_work: 0.2715 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3340 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= 0.106 Angle : 0.527 8.018 11914 Z= 0.260 Chirality : 0.043 0.238 1380 Planarity : 0.004 0.057 1496 Dihedral : 5.966 58.489 1791 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.23 % Rotamer: Outliers : 1.12 % Allowed : 11.88 % 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 (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: 0.26 (0.27), residues: 1047 helix: 0.63 (0.50), residues: 109 sheet: 0.79 (0.27), residues: 377 loop : -0.29 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.004 0.001 HIS L 91 PHE 0.010 0.001 PHE B 321 TYR 0.011 0.001 TYR A 261 ARG 0.003 0.000 ARG B 155 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 11) link_NAG-ASN : angle 1.51926 ( 33) link_ALPHA1-6 : bond 0.00087 ( 1) link_ALPHA1-6 : angle 1.72155 ( 3) link_BETA1-4 : bond 0.00296 ( 17) link_BETA1-4 : angle 1.51078 ( 51) link_ALPHA1-3 : bond 0.00590 ( 3) link_ALPHA1-3 : angle 1.43827 ( 9) hydrogen bonds : bond 0.03098 ( 282) hydrogen bonds : angle 5.22753 ( 732) SS BOND : bond 0.00317 ( 9) SS BOND : angle 0.74709 ( 18) covalent geometry : bond 0.00257 ( 8696) covalent geometry : angle 0.51062 (11800) *********************** 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: 10 poor density : 74 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7863 (mm-30) REVERT: A 363 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.6635 (mp10) REVERT: B 68 ASP cc_start: 0.7375 (p0) cc_final: 0.7084 (p0) REVERT: B 69 ILE cc_start: 0.8414 (mp) cc_final: 0.8172 (mp) REVERT: B 140 GLU cc_start: 0.8251 (tp30) cc_final: 0.8007 (mp0) REVERT: B 402 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7941 (t0) REVERT: H 58 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8475 (t70) REVERT: H 75 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8067 (mm-40) REVERT: H 83 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8230 (tm-30) REVERT: L 17 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7754 (mt-10) REVERT: L 105 GLU cc_start: 0.4937 (tm-30) cc_final: 0.4372 (mm-30) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 3.2764 time to fit residues: 272.3740 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 : 1.491 ------------------------------------------------------------------------------- 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 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 B residue 402 ASP Chi-restraints excluded: chain H residue 58 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.093327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.064831 restraints weight = 34635.501| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.46 r_work: 0.2704 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.003 0.041 8737 Z= 0.133 Angle : 0.545 8.058 11914 Z= 0.269 Chirality : 0.043 0.218 1380 Planarity : 0.004 0.057 1496 Dihedral : 5.612 57.447 1791 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 0.90 % Allowed : 12.67 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.26 (0.27), residues: 1047 helix: 0.58 (0.50), residues: 110 sheet: 0.80 (0.27), residues: 377 loop : -0.29 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 121 HIS 0.005 0.001 HIS L 91 PHE 0.012 0.001 PHE A 155 TYR 0.011 0.001 TYR A 261 ARG 0.004 0.000 ARG B 155 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 11) link_NAG-ASN : angle 1.66350 ( 33) link_ALPHA1-6 : bond 0.00026 ( 1) link_ALPHA1-6 : angle 1.72371 ( 3) link_BETA1-4 : bond 0.00308 ( 17) link_BETA1-4 : angle 1.58331 ( 51) link_ALPHA1-3 : bond 0.00525 ( 3) link_ALPHA1-3 : angle 1.41943 ( 9) hydrogen bonds : bond 0.03301 ( 282) hydrogen bonds : angle 5.22154 ( 732) SS BOND : bond 0.00348 ( 9) SS BOND : angle 0.90585 ( 18) covalent geometry : bond 0.00325 ( 8696) covalent geometry : angle 0.52716 (11800) ********************** 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 80 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.6666 (mp10) REVERT: B 68 ASP cc_start: 0.7399 (p0) cc_final: 0.7099 (p0) REVERT: B 69 ILE cc_start: 0.8346 (mp) cc_final: 0.8108 (mp) REVERT: B 140 GLU cc_start: 0.8232 (tp30) cc_final: 0.7967 (mp0) REVERT: H 58 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8498 (t70) REVERT: H 75 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8029 (mm-40) REVERT: H 83 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8228 (tm-30) REVERT: L 17 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7754 (mt-10) outliers start: 8 outliers final: 6 residues processed: 77 average time/residue: 3.2938 time to fit residues: 267.0341 Evaluate side-chains 80 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.0670 chunk 85 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.064815 restraints weight = 34717.182| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.48 r_work: 0.2707 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3440 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= 0.124 Angle : 0.538 7.537 11914 Z= 0.266 Chirality : 0.043 0.191 1380 Planarity : 0.004 0.057 1496 Dihedral : 5.303 57.218 1791 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 0.90 % Allowed : 12.56 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.25 (0.27), residues: 1047 helix: 0.58 (0.50), residues: 110 sheet: 0.80 (0.27), residues: 377 loop : -0.30 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 121 HIS 0.005 0.001 HIS L 91 PHE 0.013 0.001 PHE A 155 TYR 0.011 0.001 TYR B 133 ARG 0.004 0.000 ARG B 155 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 11) link_NAG-ASN : angle 1.58335 ( 33) link_ALPHA1-6 : bond 0.00068 ( 1) link_ALPHA1-6 : angle 1.70513 ( 3) link_BETA1-4 : bond 0.00298 ( 17) link_BETA1-4 : angle 1.57158 ( 51) link_ALPHA1-3 : bond 0.00558 ( 3) link_ALPHA1-3 : angle 1.41865 ( 9) hydrogen bonds : bond 0.03233 ( 282) hydrogen bonds : angle 5.20539 ( 732) SS BOND : bond 0.00309 ( 9) SS BOND : angle 0.86684 ( 18) covalent geometry : bond 0.00299 ( 8696) covalent geometry : angle 0.52112 (11800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11519.09 seconds wall clock time: 197 minutes 33.71 seconds (11853.71 seconds total)