Starting phenix.real_space_refine on Sun Aug 24 06:29:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9k_44387/08_2025/9b9k_44387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9k_44387/08_2025/9b9k_44387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b9k_44387/08_2025/9b9k_44387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9k_44387/08_2025/9b9k_44387.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b9k_44387/08_2025/9b9k_44387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9k_44387/08_2025/9b9k_44387.map" } resolution = 2.7 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= 0.026 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 34 5.16 5 C 5748 2.51 5 N 1474 2.21 5 O 1890 1.98 5 H 8401 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17554 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 7800 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 35, 'TRANS': 497} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 5846 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 15, 'TRANS': 361} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1856 Classifications: {'peptide': 120} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1630 Classifications: {'peptide': 112} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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: "G" 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: "I" 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: "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: 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: "N" 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: "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: 3.55, per 1000 atoms: 0.20 Number of scatterers: 17554 At special positions: 0 Unit cell: (80.784, 117.81, 131.274, 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 34 16.00 O 1890 8.00 N 1474 7.00 C 5748 6.00 H 8401 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=2.05 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 135 " distance=2.04 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 543 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.01 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 D 3 " - " MAN D 7 " " MAN D 4 " - " MAN D 5 " " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 6 " 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 I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " 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 275 " " NAG E 1 " - " ASN B 343 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN A 256 " " NAG I 1 " - " ASN A 266 " " NAG J 1 " - " ASN A 568 " " NAG K 1 " - " ASN B 192 " " NAG M 1 " - " ASN B 249 " " NAG N 1 " - " ASN B 386 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 511.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 22 sheets defined 14.0% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 196 through 203 Processing helix chain 'A' and resid 223 through 227 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 81 through 85 removed outlier: 4.286A pdb=" N GLU B 84 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 85 " --> pdb=" O THR B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 85' 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: 5.130A 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 217 removed outlier: 3.814A pdb=" N PHE B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.727A pdb=" N GLN B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 removed outlier: 3.570A pdb=" N LEU B 270 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 removed outlier: 3.503A pdb=" N GLN B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 332 removed outlier: 4.035A pdb=" N GLU B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN B 330 " --> pdb=" O LYS B 326 " (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 28 through 32 Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 27 through 29 removed outlier: 3.830A pdb=" N SER L 29 " --> pdb=" O SER L 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 27 through 29' Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.660A pdb=" N LYS A 442 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP A 432 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 422 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.915A pdb=" N SER A 120 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 108 removed outlier: 3.801A pdb=" N THR A 104 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 238 removed outlier: 6.663A pdb=" N VAL A 262 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.783A 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 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 355 through 357 removed outlier: 3.648A pdb=" N GLN A 400 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AB3, first strand: chain 'A' and resid 529 through 536 Processing sheet with id=AB4, first strand: chain 'B' and resid 66 through 69 Processing sheet with id=AB5, first strand: chain 'B' and resid 109 through 116 Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 206 removed outlier: 5.542A pdb=" N ASN B 201 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N SER B 166 " --> pdb=" O ASN B 201 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B 205 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE B 162 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B 252 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE B 314 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 254 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA B 316 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE B 256 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR B 318 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR B 258 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AB8, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.482A pdb=" N TRP H 33 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.464A pdb=" N TYR H 102 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC3, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.650A pdb=" N ILE L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 9 through 13 323 hydrogen bonds defined for protein. 810 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: 4.37 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 2004 1.02 - 1.22: 6625 1.22 - 1.42: 3803 1.42 - 1.63: 5263 1.63 - 1.83: 49 Bond restraints: 17744 Sorted by residual: bond pdb=" ND2 ASN A 266 " pdb="HD21 ASN A 266 " ideal model delta sigma weight residual 0.860 1.019 -0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" ND2 ASN A 568 " pdb="HD21 ASN A 568 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" ND2 ASN B 397 " pdb="HD21 ASN B 397 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" ND2 ASN B 192 " pdb="HD21 ASN B 192 " ideal model delta sigma weight residual 0.860 1.014 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" ND2 ASN B 386 " pdb="HD21 ASN B 386 " ideal model delta sigma weight residual 0.860 1.014 -0.154 2.00e-02 2.50e+03 5.94e+01 ... (remaining 17739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.72: 30928 5.72 - 11.45: 843 11.45 - 17.17: 1 17.17 - 22.89: 1 22.89 - 28.61: 4 Bond angle restraints: 31777 Sorted by residual: angle pdb=" O TYR B 440 " pdb=" C TYR B 440 " pdb=" N ILE B 441 " ideal model delta sigma weight residual 122.82 94.21 28.61 1.30e+00 5.92e-01 4.84e+02 angle pdb=" CA TYR B 440 " pdb=" C TYR B 440 " pdb=" N ILE B 441 " ideal model delta sigma weight residual 116.54 144.82 -28.28 1.36e+00 5.41e-01 4.32e+02 angle pdb=" C TYR B 440 " pdb=" N ILE B 441 " pdb=" CA ILE B 441 " ideal model delta sigma weight residual 121.70 147.59 -25.89 1.80e+00 3.09e-01 2.07e+02 angle pdb=" C TYR B 440 " pdb=" N ILE B 441 " pdb=" H ILE B 441 " ideal model delta sigma weight residual 124.30 100.71 23.59 3.00e+00 1.11e-01 6.18e+01 angle pdb=" CA ASP B 233 " pdb=" CB ASP B 233 " pdb=" CG ASP B 233 " ideal model delta sigma weight residual 112.60 119.90 -7.30 1.00e+00 1.00e+00 5.32e+01 ... (remaining 31772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 8218 21.71 - 43.42: 431 43.42 - 65.13: 194 65.13 - 86.84: 72 86.84 - 108.55: 24 Dihedral angle restraints: 8939 sinusoidal: 5105 harmonic: 3834 Sorted by residual: dihedral pdb=" CB CYS B 381 " pdb=" SG CYS B 381 " pdb=" SG CYS B 395 " pdb=" CB CYS B 395 " ideal model delta sinusoidal sigma weight residual -86.00 -158.44 72.44 1 1.00e+01 1.00e-02 6.70e+01 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 -86.00 -25.86 -60.14 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CA GLN H 105 " pdb=" C GLN H 105 " pdb=" N GLY H 106 " pdb=" CA GLY H 106 " ideal model delta harmonic sigma weight residual 180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 8936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 1414 0.222 - 0.443: 64 0.443 - 0.665: 3 0.665 - 0.887: 0 0.887 - 1.108: 1 Chirality restraints: 1482 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-02 2.50e+03 5.21e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.42e+02 chirality pdb=" C1 MAN D 7 " pdb=" O3 BMA D 3 " pdb=" C2 MAN D 7 " pdb=" O5 MAN D 7 " both_signs ideal model delta sigma weight residual False 2.40 2.06 0.34 2.00e-02 2.50e+03 2.95e+02 ... (remaining 1479 not shown) Planarity restraints: 2697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 574 " 0.174 2.00e-02 2.50e+03 4.22e-01 2.67e+03 pdb=" CD GLN A 574 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN A 574 " -0.169 2.00e-02 2.50e+03 pdb=" NE2 GLN A 574 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 574 " -0.706 2.00e-02 2.50e+03 pdb="HE22 GLN A 574 " 0.715 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.367 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" C7 NAG G 1 " -0.094 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.548 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.339 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG N 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.506 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.078 2.00e-02 2.50e+03 ... (remaining 2694 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1117 2.19 - 2.79: 30229 2.79 - 3.39: 48364 3.39 - 4.00: 66536 4.00 - 4.60: 96915 Nonbonded interactions: 243161 Sorted by model distance: nonbonded pdb=" OD1 ASP H 72 " pdb=" HG SER H 74 " model vdw 1.585 2.450 nonbonded pdb=" OD2 ASP B 120 " pdb=" HG SER B 158 " model vdw 1.591 2.450 nonbonded pdb=" OE1 GLU A 320 " pdb=" HG SER B 298 " model vdw 1.610 2.450 nonbonded pdb=" OE2 GLU A 207 " pdb=" HG1 THR H 52A" model vdw 1.625 2.450 nonbonded pdb="HD21 ASN A 43 " pdb=" C2 NAG C 1 " model vdw 1.636 2.200 ... (remaining 243156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' } 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=0.00 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: 2.860 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: 0.050 Set scattering table: 0.050 Process input model: 18.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.013 0.085 9384 Z= 0.762 Angle : 1.989 28.613 12793 Z= 1.281 Chirality : 0.112 1.108 1482 Planarity : 0.024 0.311 1609 Dihedral : 16.996 108.551 3869 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.10 % Allowed : 1.57 % Favored : 98.32 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.79 (0.23), residues: 1128 helix: -2.37 (0.38), residues: 103 sheet: 0.54 (0.27), residues: 303 loop : -0.70 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 66 TYR 0.100 0.020 TYR L 31 PHE 0.068 0.014 PHE A 172 TRP 0.140 0.025 TRP B 247 HIS 0.013 0.004 HIS H 3 Details of bonding type rmsd covalent geometry : bond 0.01252 ( 9343) covalent geometry : angle 1.96368 (12679) SS BOND : bond 0.01259 ( 9) SS BOND : angle 2.33430 ( 18) hydrogen bonds : bond 0.15494 ( 313) hydrogen bonds : angle 8.08968 ( 810) link_ALPHA1-3 : bond 0.03969 ( 3) link_ALPHA1-3 : angle 2.43395 ( 9) link_ALPHA1-6 : bond 0.03900 ( 2) link_ALPHA1-6 : angle 5.18607 ( 6) link_BETA1-4 : bond 0.02404 ( 16) link_BETA1-4 : angle 3.58677 ( 48) link_NAG-ASN : bond 0.02244 ( 11) link_NAG-ASN : angle 4.92400 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 457 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.518 Fit side-chains REVERT: A 126 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7519 (pm20) REVERT: B 77 ASN cc_start: 0.7115 (m-40) cc_final: 0.6182 (p0) REVERT: B 119 GLU cc_start: 0.8516 (tp30) cc_final: 0.8188 (mp0) REVERT: B 285 ASN cc_start: 0.8347 (m-40) cc_final: 0.7881 (t0) REVERT: B 287 MET cc_start: 0.8257 (mmm) cc_final: 0.8037 (tpp) REVERT: B 348 ILE cc_start: 0.8567 (mt) cc_final: 0.8150 (mm) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 1.7473 time to fit residues: 200.3370 Evaluate side-chains 61 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 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 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.091183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.064957 restraints weight = 47247.521| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.85 r_work: 0.2817 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9384 Z= 0.190 Angle : 0.790 9.269 12793 Z= 0.401 Chirality : 0.048 0.253 1482 Planarity : 0.005 0.044 1609 Dihedral : 13.012 78.301 1884 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.57 % Allowed : 6.71 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.82 (0.23), residues: 1128 helix: -1.71 (0.42), residues: 106 sheet: 0.06 (0.24), residues: 386 loop : -0.66 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 155 TYR 0.018 0.002 TYR L 49 PHE 0.017 0.002 PHE H 29 TRP 0.013 0.002 TRP H 103 HIS 0.007 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 9343) covalent geometry : angle 0.75990 (12679) SS BOND : bond 0.00696 ( 9) SS BOND : angle 1.07063 ( 18) hydrogen bonds : bond 0.05227 ( 313) hydrogen bonds : angle 6.68935 ( 810) link_ALPHA1-3 : bond 0.01110 ( 3) link_ALPHA1-3 : angle 2.28669 ( 9) link_ALPHA1-6 : bond 0.00544 ( 2) link_ALPHA1-6 : angle 1.50390 ( 6) link_BETA1-4 : bond 0.00392 ( 16) link_BETA1-4 : angle 2.46624 ( 48) link_NAG-ASN : bond 0.00618 ( 11) link_NAG-ASN : angle 2.93820 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 457 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7315 (pm20) REVERT: A 271 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7656 (ttp80) REVERT: A 546 MET cc_start: 0.6414 (mpp) cc_final: 0.6124 (mpp) REVERT: B 77 ASN cc_start: 0.7556 (m-40) cc_final: 0.7145 (p0) REVERT: B 285 ASN cc_start: 0.8476 (m-40) cc_final: 0.8059 (t0) outliers start: 15 outliers final: 6 residues processed: 71 average time/residue: 1.3300 time to fit residues: 101.3989 Evaluate side-chains 61 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.061979 restraints weight = 47810.702| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.88 r_work: 0.2760 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9384 Z= 0.197 Angle : 0.678 8.722 12793 Z= 0.338 Chirality : 0.047 0.181 1482 Planarity : 0.005 0.050 1609 Dihedral : 8.500 64.680 1884 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.36 % Allowed : 8.49 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.81 (0.23), residues: 1128 helix: -1.18 (0.45), residues: 106 sheet: 0.04 (0.24), residues: 390 loop : -0.75 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 423 TYR 0.015 0.002 TYR A 261 PHE 0.017 0.002 PHE A 172 TRP 0.008 0.001 TRP A 188 HIS 0.002 0.001 HIS H 3 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 9343) covalent geometry : angle 0.65819 (12679) SS BOND : bond 0.01129 ( 9) SS BOND : angle 1.19191 ( 18) hydrogen bonds : bond 0.04277 ( 313) hydrogen bonds : angle 5.88112 ( 810) link_ALPHA1-3 : bond 0.01159 ( 3) link_ALPHA1-3 : angle 2.32956 ( 9) link_ALPHA1-6 : bond 0.00308 ( 2) link_ALPHA1-6 : angle 1.68743 ( 6) link_BETA1-4 : bond 0.00425 ( 16) link_BETA1-4 : angle 1.93320 ( 48) link_NAG-ASN : bond 0.00345 ( 11) link_NAG-ASN : angle 1.82980 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 457 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7760 (pm20) REVERT: A 546 MET cc_start: 0.6301 (mpp) cc_final: 0.5878 (mpp) REVERT: A 578 ASP cc_start: 0.6661 (m-30) cc_final: 0.6208 (m-30) REVERT: B 77 ASN cc_start: 0.7759 (m-40) cc_final: 0.7426 (p0) REVERT: B 285 ASN cc_start: 0.8605 (m-40) cc_final: 0.8270 (t0) REVERT: B 378 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7898 (mttp) outliers start: 13 outliers final: 6 residues processed: 69 average time/residue: 1.3267 time to fit residues: 97.9533 Evaluate side-chains 63 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 48 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 100 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.062035 restraints weight = 47757.832| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.90 r_work: 0.2729 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9384 Z= 0.149 Angle : 0.609 7.763 12793 Z= 0.304 Chirality : 0.045 0.192 1482 Planarity : 0.004 0.037 1609 Dihedral : 7.427 61.034 1882 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.26 % Allowed : 9.43 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.63 (0.24), residues: 1128 helix: -0.80 (0.48), residues: 106 sheet: 0.12 (0.24), residues: 390 loop : -0.65 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 154 TYR 0.014 0.001 TYR A 261 PHE 0.022 0.001 PHE H 29 TRP 0.007 0.001 TRP H 103 HIS 0.002 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9343) covalent geometry : angle 0.59240 (12679) SS BOND : bond 0.00517 ( 9) SS BOND : angle 0.88027 ( 18) hydrogen bonds : bond 0.03816 ( 313) hydrogen bonds : angle 5.71521 ( 810) link_ALPHA1-3 : bond 0.01015 ( 3) link_ALPHA1-3 : angle 2.36428 ( 9) link_ALPHA1-6 : bond 0.00305 ( 2) link_ALPHA1-6 : angle 1.75430 ( 6) link_BETA1-4 : bond 0.00315 ( 16) link_BETA1-4 : angle 1.67279 ( 48) link_NAG-ASN : bond 0.00220 ( 11) link_NAG-ASN : angle 1.55856 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 457 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.491 Fit side-chains REVERT: A 126 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7670 (pm20) REVERT: A 284 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: A 546 MET cc_start: 0.6156 (mpp) cc_final: 0.5641 (mpp) REVERT: A 578 ASP cc_start: 0.6586 (m-30) cc_final: 0.6257 (m-30) REVERT: B 77 ASN cc_start: 0.7844 (m-40) cc_final: 0.7455 (p0) REVERT: B 285 ASN cc_start: 0.8650 (m-40) cc_final: 0.8321 (t0) REVERT: B 361 GLU cc_start: 0.8644 (tt0) cc_final: 0.8349 (tp30) REVERT: B 378 LYS cc_start: 0.8285 (mtmm) cc_final: 0.7908 (mttp) outliers start: 12 outliers final: 7 residues processed: 69 average time/residue: 1.1719 time to fit residues: 87.2409 Evaluate side-chains 67 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.059509 restraints weight = 47807.959| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.88 r_work: 0.2709 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9384 Z= 0.257 Angle : 0.649 8.203 12793 Z= 0.326 Chirality : 0.046 0.186 1482 Planarity : 0.004 0.035 1609 Dihedral : 7.248 59.589 1882 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.89 % Allowed : 9.43 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.69 (0.24), residues: 1128 helix: -0.74 (0.48), residues: 106 sheet: 0.10 (0.24), residues: 390 loop : -0.73 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 32 TYR 0.016 0.002 TYR A 261 PHE 0.016 0.002 PHE H 29 TRP 0.009 0.002 TRP B 247 HIS 0.008 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 9343) covalent geometry : angle 0.63180 (12679) SS BOND : bond 0.00926 ( 9) SS BOND : angle 1.11363 ( 18) hydrogen bonds : bond 0.04223 ( 313) hydrogen bonds : angle 5.68418 ( 810) link_ALPHA1-3 : bond 0.00928 ( 3) link_ALPHA1-3 : angle 2.42814 ( 9) link_ALPHA1-6 : bond 0.00209 ( 2) link_ALPHA1-6 : angle 1.77268 ( 6) link_BETA1-4 : bond 0.00337 ( 16) link_BETA1-4 : angle 1.57167 ( 48) link_NAG-ASN : bond 0.00388 ( 11) link_NAG-ASN : angle 1.85038 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 457 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6811 (mt0) cc_final: 0.6357 (mm-40) REVERT: A 271 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7737 (mtp-110) REVERT: A 546 MET cc_start: 0.6264 (mpp) cc_final: 0.5744 (mpp) REVERT: A 578 ASP cc_start: 0.6913 (m-30) cc_final: 0.6621 (m-30) REVERT: B 77 ASN cc_start: 0.7834 (m-40) cc_final: 0.7407 (p0) REVERT: B 285 ASN cc_start: 0.8748 (m-40) cc_final: 0.8447 (t0) REVERT: B 378 LYS cc_start: 0.8348 (mtmm) cc_final: 0.7945 (mttp) REVERT: H 58 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8553 (mt-10) REVERT: L 103 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8098 (ttmm) outliers start: 18 outliers final: 14 residues processed: 73 average time/residue: 1.1640 time to fit residues: 90.9940 Evaluate side-chains 73 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 75 optimal weight: 0.0270 chunk 97 optimal weight: 0.9980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN A 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.087256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.061201 restraints weight = 47257.995| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.90 r_work: 0.2747 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9384 Z= 0.113 Angle : 0.567 6.985 12793 Z= 0.284 Chirality : 0.044 0.203 1482 Planarity : 0.004 0.035 1609 Dihedral : 6.672 56.342 1882 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.26 % Allowed : 11.01 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.51 (0.24), residues: 1128 helix: -0.49 (0.49), residues: 106 sheet: 0.19 (0.25), residues: 384 loop : -0.59 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 154 TYR 0.014 0.001 TYR L 49 PHE 0.017 0.001 PHE H 29 TRP 0.009 0.001 TRP A 188 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9343) covalent geometry : angle 0.55285 (12679) SS BOND : bond 0.00604 ( 9) SS BOND : angle 0.95584 ( 18) hydrogen bonds : bond 0.03504 ( 313) hydrogen bonds : angle 5.49271 ( 810) link_ALPHA1-3 : bond 0.00938 ( 3) link_ALPHA1-3 : angle 2.06442 ( 9) link_ALPHA1-6 : bond 0.00419 ( 2) link_ALPHA1-6 : angle 1.82315 ( 6) link_BETA1-4 : bond 0.00278 ( 16) link_BETA1-4 : angle 1.38536 ( 48) link_NAG-ASN : bond 0.00177 ( 11) link_NAG-ASN : angle 1.44431 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 457 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.469 Fit side-chains REVERT: A 66 GLN cc_start: 0.6804 (mt0) cc_final: 0.6330 (mm-40) REVERT: A 271 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7695 (mtp-110) REVERT: A 284 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: A 546 MET cc_start: 0.6174 (mpp) cc_final: 0.5679 (mpp) REVERT: A 578 ASP cc_start: 0.6749 (m-30) cc_final: 0.6431 (m-30) REVERT: B 77 ASN cc_start: 0.7872 (m-40) cc_final: 0.7396 (p0) REVERT: B 285 ASN cc_start: 0.8761 (m-40) cc_final: 0.8483 (t0) REVERT: B 378 LYS cc_start: 0.8302 (mtmm) cc_final: 0.7881 (mttp) REVERT: H 58 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8519 (mt-10) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 1.1059 time to fit residues: 81.1777 Evaluate side-chains 63 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 91 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.061254 restraints weight = 47689.537| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.89 r_work: 0.2709 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9384 Z= 0.130 Angle : 0.565 7.058 12793 Z= 0.282 Chirality : 0.043 0.204 1482 Planarity : 0.004 0.034 1609 Dihedral : 6.452 57.298 1882 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.36 % Allowed : 11.53 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.43 (0.24), residues: 1128 helix: -0.39 (0.50), residues: 106 sheet: 0.28 (0.25), residues: 382 loop : -0.57 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 317 TYR 0.013 0.001 TYR L 49 PHE 0.015 0.001 PHE H 29 TRP 0.008 0.001 TRP A 188 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9343) covalent geometry : angle 0.55119 (12679) SS BOND : bond 0.00624 ( 9) SS BOND : angle 0.98827 ( 18) hydrogen bonds : bond 0.03433 ( 313) hydrogen bonds : angle 5.40566 ( 810) link_ALPHA1-3 : bond 0.00854 ( 3) link_ALPHA1-3 : angle 2.05228 ( 9) link_ALPHA1-6 : bond 0.00377 ( 2) link_ALPHA1-6 : angle 1.77386 ( 6) link_BETA1-4 : bond 0.00287 ( 16) link_BETA1-4 : angle 1.37711 ( 48) link_NAG-ASN : bond 0.00187 ( 11) link_NAG-ASN : angle 1.43852 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 457 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.449 Fit side-chains REVERT: A 66 GLN cc_start: 0.6863 (mt0) cc_final: 0.6403 (mm-40) REVERT: A 271 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7820 (mtp-110) REVERT: A 284 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: A 546 MET cc_start: 0.6141 (mpp) cc_final: 0.5655 (mpp) REVERT: A 578 ASP cc_start: 0.6932 (m-30) cc_final: 0.6618 (m-30) REVERT: B 77 ASN cc_start: 0.7872 (m-40) cc_final: 0.7422 (p0) REVERT: B 285 ASN cc_start: 0.8742 (m-40) cc_final: 0.8459 (t0) REVERT: B 361 GLU cc_start: 0.8749 (tt0) cc_final: 0.8338 (tp30) REVERT: B 378 LYS cc_start: 0.8357 (mtmm) cc_final: 0.7946 (mttp) REVERT: H 58 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8558 (mt-10) REVERT: L 103 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8148 (ttmm) outliers start: 13 outliers final: 6 residues processed: 63 average time/residue: 1.2041 time to fit residues: 81.2830 Evaluate side-chains 62 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.062044 restraints weight = 47076.406| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.89 r_work: 0.2768 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9384 Z= 0.108 Angle : 0.539 6.638 12793 Z= 0.268 Chirality : 0.043 0.214 1482 Planarity : 0.003 0.034 1609 Dihedral : 6.021 57.011 1882 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.15 % Allowed : 11.64 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.27 (0.25), residues: 1128 helix: -0.24 (0.50), residues: 106 sheet: 0.36 (0.25), residues: 387 loop : -0.46 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 154 TYR 0.013 0.001 TYR L 49 PHE 0.015 0.001 PHE H 29 TRP 0.007 0.001 TRP A 188 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9343) covalent geometry : angle 0.52571 (12679) SS BOND : bond 0.00811 ( 9) SS BOND : angle 0.97224 ( 18) hydrogen bonds : bond 0.03174 ( 313) hydrogen bonds : angle 5.24515 ( 810) link_ALPHA1-3 : bond 0.00887 ( 3) link_ALPHA1-3 : angle 1.97124 ( 9) link_ALPHA1-6 : bond 0.00516 ( 2) link_ALPHA1-6 : angle 1.82960 ( 6) link_BETA1-4 : bond 0.00297 ( 16) link_BETA1-4 : angle 1.31152 ( 48) link_NAG-ASN : bond 0.00175 ( 11) link_NAG-ASN : angle 1.26927 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 457 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6873 (mt0) cc_final: 0.6418 (mm-40) REVERT: A 271 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7808 (mtp-110) REVERT: A 284 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: A 546 MET cc_start: 0.6132 (mpp) cc_final: 0.5641 (mpp) REVERT: A 578 ASP cc_start: 0.7002 (m-30) cc_final: 0.6637 (m-30) REVERT: B 285 ASN cc_start: 0.8720 (m-40) cc_final: 0.8446 (t0) REVERT: B 290 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8145 (mtp) REVERT: B 361 GLU cc_start: 0.8714 (tt0) cc_final: 0.8290 (tp30) REVERT: B 378 LYS cc_start: 0.8321 (mtmm) cc_final: 0.7938 (mttp) REVERT: H 58 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8532 (mt-10) REVERT: L 103 LYS cc_start: 0.8411 (ttmm) cc_final: 0.8153 (ttmm) outliers start: 11 outliers final: 7 residues processed: 63 average time/residue: 1.1618 time to fit residues: 78.2503 Evaluate side-chains 65 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 109 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.087280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.061254 restraints weight = 47442.856| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.89 r_work: 0.2715 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9384 Z= 0.168 Angle : 0.557 6.963 12793 Z= 0.277 Chirality : 0.043 0.206 1482 Planarity : 0.003 0.034 1609 Dihedral : 6.067 58.815 1882 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.15 % Allowed : 11.64 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.28 (0.25), residues: 1128 helix: -0.22 (0.50), residues: 106 sheet: 0.34 (0.25), residues: 397 loop : -0.48 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 154 TYR 0.013 0.001 TYR L 49 PHE 0.013 0.001 PHE H 29 TRP 0.007 0.001 TRP H 103 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9343) covalent geometry : angle 0.54299 (12679) SS BOND : bond 0.00695 ( 9) SS BOND : angle 1.00926 ( 18) hydrogen bonds : bond 0.03382 ( 313) hydrogen bonds : angle 5.25035 ( 810) link_ALPHA1-3 : bond 0.00828 ( 3) link_ALPHA1-3 : angle 2.08487 ( 9) link_ALPHA1-6 : bond 0.00441 ( 2) link_ALPHA1-6 : angle 1.79204 ( 6) link_BETA1-4 : bond 0.00291 ( 16) link_BETA1-4 : angle 1.33465 ( 48) link_NAG-ASN : bond 0.00217 ( 11) link_NAG-ASN : angle 1.38498 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 457 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.374 Fit side-chains REVERT: A 66 GLN cc_start: 0.6943 (mt0) cc_final: 0.6480 (mm-40) REVERT: A 271 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7798 (mtp-110) REVERT: A 284 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: A 546 MET cc_start: 0.6173 (mpp) cc_final: 0.5691 (mpp) REVERT: A 578 ASP cc_start: 0.7029 (m-30) cc_final: 0.6703 (m-30) REVERT: B 285 ASN cc_start: 0.8745 (m-40) cc_final: 0.8480 (t0) REVERT: B 290 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8194 (mtp) REVERT: B 361 GLU cc_start: 0.8760 (tt0) cc_final: 0.8339 (tp30) REVERT: B 378 LYS cc_start: 0.8368 (mtmm) cc_final: 0.7979 (mttp) REVERT: H 58 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8560 (mt-10) REVERT: L 103 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8209 (ttmm) outliers start: 11 outliers final: 7 residues processed: 61 average time/residue: 1.0975 time to fit residues: 71.5343 Evaluate side-chains 65 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.061606 restraints weight = 47096.954| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.88 r_work: 0.2726 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9384 Z= 0.124 Angle : 0.546 6.767 12793 Z= 0.272 Chirality : 0.043 0.208 1482 Planarity : 0.003 0.034 1609 Dihedral : 5.975 58.651 1882 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.94 % Allowed : 11.74 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.23 (0.25), residues: 1128 helix: -0.18 (0.50), residues: 106 sheet: 0.39 (0.25), residues: 388 loop : -0.44 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 154 TYR 0.013 0.001 TYR L 49 PHE 0.014 0.001 PHE H 29 TRP 0.007 0.001 TRP A 188 HIS 0.002 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9343) covalent geometry : angle 0.53243 (12679) SS BOND : bond 0.00954 ( 9) SS BOND : angle 1.17577 ( 18) hydrogen bonds : bond 0.03232 ( 313) hydrogen bonds : angle 5.22204 ( 810) link_ALPHA1-3 : bond 0.00813 ( 3) link_ALPHA1-3 : angle 1.98577 ( 9) link_ALPHA1-6 : bond 0.00496 ( 2) link_ALPHA1-6 : angle 1.81711 ( 6) link_BETA1-4 : bond 0.00282 ( 16) link_BETA1-4 : angle 1.32626 ( 48) link_NAG-ASN : bond 0.00174 ( 11) link_NAG-ASN : angle 1.31909 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 457 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.7005 (mt0) cc_final: 0.6558 (mm-40) REVERT: A 271 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7757 (mtp-110) REVERT: A 546 MET cc_start: 0.6174 (mpp) cc_final: 0.5693 (mpp) REVERT: A 578 ASP cc_start: 0.6978 (m-30) cc_final: 0.6652 (m-30) REVERT: B 285 ASN cc_start: 0.8737 (m-40) cc_final: 0.8471 (t0) REVERT: B 290 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8158 (mtp) REVERT: B 361 GLU cc_start: 0.8731 (tt0) cc_final: 0.8310 (tp30) REVERT: B 378 LYS cc_start: 0.8326 (mtmm) cc_final: 0.7941 (mttp) REVERT: H 58 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8544 (mt-10) REVERT: L 85 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8565 (t0) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 1.1343 time to fit residues: 74.0307 Evaluate side-chains 64 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.061310 restraints weight = 47487.529| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.89 r_work: 0.2733 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9384 Z= 0.145 Angle : 0.551 6.970 12793 Z= 0.274 Chirality : 0.043 0.207 1482 Planarity : 0.003 0.034 1609 Dihedral : 5.949 59.428 1882 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.94 % Allowed : 11.64 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.23 (0.25), residues: 1128 helix: -0.17 (0.50), residues: 106 sheet: 0.40 (0.25), residues: 395 loop : -0.45 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 154 TYR 0.013 0.001 TYR L 49 PHE 0.013 0.001 PHE H 29 TRP 0.007 0.001 TRP A 188 HIS 0.002 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9343) covalent geometry : angle 0.53733 (12679) SS BOND : bond 0.00797 ( 9) SS BOND : angle 1.14306 ( 18) hydrogen bonds : bond 0.03299 ( 313) hydrogen bonds : angle 5.20688 ( 810) link_ALPHA1-3 : bond 0.00788 ( 3) link_ALPHA1-3 : angle 1.98902 ( 9) link_ALPHA1-6 : bond 0.00490 ( 2) link_ALPHA1-6 : angle 1.79965 ( 6) link_BETA1-4 : bond 0.00292 ( 16) link_BETA1-4 : angle 1.32698 ( 48) link_NAG-ASN : bond 0.00195 ( 11) link_NAG-ASN : angle 1.35602 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5755.60 seconds wall clock time: 98 minutes 14.46 seconds (5894.46 seconds total)