Starting phenix.real_space_refine on Sat Jul 4 02:13:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9k_44387/07_2026/9b9k_44387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9k_44387/07_2026/9b9k_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b9k_44387/07_2026/9b9k_44387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9k_44387/07_2026/9b9k_44387.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9k_44387/07_2026/9b9k_44387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9k_44387/07_2026/9b9k_44387.cif" } 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 14 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.87, per 1000 atoms: 0.16 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: 1.45 Conformation dependent library (CDL) restraints added in 492.4 milliseconds 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: 0.46 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: 3.93 Time building geometry restraints manager: 1.94 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: 4.310 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: 0.130 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.410 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: 0.000 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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 are 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/Z covalent geometry : bond 0.01252 / 0.76 ( 9343) covalent geometry : angle 1.96368 / 1.28 (12679) SS BOND : bond 0.01259 / 0.54 ( 9) SS BOND : angle 2.33430 / 1.41 ( 18) hydrogen bonds : bond 0.15494 / 10.80 ( 313) hydrogen bonds : angle 8.08968 / 5.71 ( 810) link_ALPHA1-3 : bond 0.03969 / 1.99 ( 3) link_ALPHA1-3 : angle 2.43395 / 1.42 ( 9) link_ALPHA1-6 : bond 0.03900 / 1.96 ( 2) link_ALPHA1-6 : angle 5.18607 / 3.27 ( 6) link_BETA1-4 : bond 0.02404 / 1.28 ( 16) link_BETA1-4 : angle 3.58677 / 2.15 ( 48) link_NAG-ASN : bond 0.02244 / 1.03 ( 11) link_NAG-ASN : angle 4.92400 / 3.22 ( 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 : 0.326 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: 1.3372 time to fit residues: 154.3467 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 : 0.464 ------------------------------------------------------------------------------- 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... B 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.064995 restraints weight = 47142.252| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.85 r_work: 0.2797 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 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 = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9384 Z= 0.205 Angle : 0.798 9.008 12793 Z= 0.405 Chirality : 0.049 0.230 1482 Planarity : 0.005 0.043 1609 Dihedral : 12.919 78.157 1884 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.36 % Allowed : 7.02 % Favored : 91.61 % 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 are not related in a simple way. whole: -0.86 (0.23), residues: 1128 helix: -1.69 (0.42), residues: 106 sheet: 0.06 (0.24), residues: 386 loop : -0.72 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 155 TYR 0.019 0.002 TYR L 49 PHE 0.016 0.002 PHE H 29 TRP 0.012 0.002 TRP H 103 HIS 0.007 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 ( 9343) covalent geometry : angle 0.76866 / 0.40 (12679) SS BOND : bond 0.01332 / 0.66 ( 9) SS BOND : angle 1.23604 / 0.72 ( 18) hydrogen bonds : bond 0.05265 / 3.44 ( 313) hydrogen bonds : angle 6.68578 / 4.64 ( 810) link_ALPHA1-3 : bond 0.00841 / 0.44 ( 3) link_ALPHA1-3 : angle 2.18150 / 1.40 ( 9) link_ALPHA1-6 : bond 0.00343 / 0.17 ( 2) link_ALPHA1-6 : angle 1.46467 / 1.03 ( 6) link_BETA1-4 : bond 0.00389 / 0.24 ( 16) link_BETA1-4 : angle 2.46819 / 1.47 ( 48) link_NAG-ASN : bond 0.00657 / 0.29 ( 11) link_NAG-ASN : angle 2.92171 / 1.85 ( 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: 13 poor density : 68 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7307 (pm20) REVERT: A 271 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7655 (ttp80) REVERT: A 546 MET cc_start: 0.6426 (mpp) cc_final: 0.6039 (mpp) REVERT: B 77 ASN cc_start: 0.7537 (m-40) cc_final: 0.7137 (p0) REVERT: B 285 ASN cc_start: 0.8466 (m-40) cc_final: 0.8122 (t0) outliers start: 13 outliers final: 6 residues processed: 72 average time/residue: 1.0692 time to fit residues: 83.3962 Evaluate side-chains 62 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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: 0.9980 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 4 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.090531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.064417 restraints weight = 47215.648| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.87 r_work: 0.2769 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9384 Z= 0.133 Angle : 0.650 8.515 12793 Z= 0.325 Chirality : 0.047 0.230 1482 Planarity : 0.004 0.040 1609 Dihedral : 9.248 67.965 1884 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.36 % Allowed : 7.76 % Favored : 90.88 % 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 are not related in a simple way. whole: -0.75 (0.23), residues: 1128 helix: -1.22 (0.45), residues: 106 sheet: 0.09 (0.24), residues: 381 loop : -0.69 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 423 TYR 0.014 0.001 TYR A 261 PHE 0.015 0.001 PHE H 29 TRP 0.009 0.001 TRP A 188 HIS 0.009 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9343) covalent geometry : angle 0.63205 / 0.32 (12679) SS BOND : bond 0.01096 / 0.54 ( 9) SS BOND : angle 0.90278 / 0.54 ( 18) hydrogen bonds : bond 0.04081 / 2.66 ( 313) hydrogen bonds : angle 5.99053 / 4.14 ( 810) link_ALPHA1-3 : bond 0.01049 / 0.54 ( 3) link_ALPHA1-3 : angle 2.12873 / 1.36 ( 9) link_ALPHA1-6 : bond 0.00367 / 0.18 ( 2) link_ALPHA1-6 : angle 1.61612 / 1.09 ( 6) link_BETA1-4 : bond 0.00419 / 0.24 ( 16) link_BETA1-4 : angle 1.90714 / 1.13 ( 48) link_NAG-ASN : bond 0.00308 / 0.15 ( 11) link_NAG-ASN : angle 1.61628 / 1.00 ( 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 73 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7465 (pm20) REVERT: A 271 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7673 (ttp80) REVERT: A 546 MET cc_start: 0.6355 (mpp) cc_final: 0.5778 (mpp) REVERT: B 77 ASN cc_start: 0.7905 (m-40) cc_final: 0.7399 (p0) REVERT: B 285 ASN cc_start: 0.8511 (m-40) cc_final: 0.8120 (t0) REVERT: B 287 MET cc_start: 0.8524 (mmm) cc_final: 0.8317 (tpp) outliers start: 13 outliers final: 4 residues processed: 66 average time/residue: 1.1186 time to fit residues: 79.4264 Evaluate side-chains 57 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain H residue 57 THR 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: 0.9980 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.062177 restraints weight = 47318.074| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.91 r_work: 0.2735 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 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 = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9384 Z= 0.179 Angle : 0.620 8.666 12793 Z= 0.310 Chirality : 0.045 0.193 1482 Planarity : 0.004 0.040 1609 Dihedral : 7.166 59.865 1882 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.57 % Allowed : 8.60 % Favored : 89.83 % 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 are not related in a simple way. whole: -0.63 (0.24), residues: 1128 helix: -0.72 (0.48), residues: 107 sheet: 0.15 (0.24), residues: 390 loop : -0.68 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 154 TYR 0.015 0.002 TYR L 49 PHE 0.028 0.002 PHE H 29 TRP 0.007 0.001 TRP A 188 HIS 0.010 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 9343) covalent geometry : angle 0.60292 / 0.31 (12679) SS BOND : bond 0.00712 / 0.35 ( 9) SS BOND : angle 0.95862 / 0.58 ( 18) hydrogen bonds : bond 0.03908 / 2.56 ( 313) hydrogen bonds : angle 5.64895 / 3.88 ( 810) link_ALPHA1-3 : bond 0.00954 / 0.49 ( 3) link_ALPHA1-3 : angle 2.43799 / 1.55 ( 9) link_ALPHA1-6 : bond 0.00308 / 0.15 ( 2) link_ALPHA1-6 : angle 1.76262 / 1.10 ( 6) link_BETA1-4 : bond 0.00342 / 0.19 ( 16) link_BETA1-4 : angle 1.66623 / 0.99 ( 48) link_NAG-ASN : bond 0.00317 / 0.14 ( 11) link_NAG-ASN : angle 1.64941 / 0.95 ( 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 75 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.343 Fit side-chains REVERT: A 126 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7652 (pm20) REVERT: A 284 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: A 546 MET cc_start: 0.6161 (mpp) cc_final: 0.5631 (mpp) REVERT: A 578 ASP cc_start: 0.6620 (m-30) cc_final: 0.6228 (m-30) REVERT: B 77 ASN cc_start: 0.7908 (m-40) cc_final: 0.7492 (p0) REVERT: B 285 ASN cc_start: 0.8633 (m-40) cc_final: 0.8299 (t0) outliers start: 15 outliers final: 7 residues processed: 67 average time/residue: 1.1337 time to fit residues: 81.8208 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 : 0.486 ------------------------------------------------------------------------------- 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: 0.9980 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3313 r_free = 0.3313 target = 0.087947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.061712 restraints weight = 46956.781| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.92 r_work: 0.2732 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 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 = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9384 Z= 0.162 Angle : 0.593 7.383 12793 Z= 0.297 Chirality : 0.044 0.199 1482 Planarity : 0.004 0.061 1609 Dihedral : 6.691 55.915 1882 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.36 % Allowed : 9.96 % 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 are not related in a simple way. whole: -0.55 (0.24), residues: 1128 helix: -0.51 (0.49), residues: 106 sheet: 0.22 (0.25), residues: 390 loop : -0.68 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 271 TYR 0.014 0.001 TYR A 261 PHE 0.013 0.001 PHE B 321 TRP 0.007 0.001 TRP A 188 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 9343) covalent geometry : angle 0.57978 / 0.29 (12679) SS BOND : bond 0.00866 / 0.43 ( 9) SS BOND : angle 0.93111 / 0.56 ( 18) hydrogen bonds : bond 0.03695 / 2.43 ( 313) hydrogen bonds : angle 5.50184 / 3.78 ( 810) link_ALPHA1-3 : bond 0.00940 / 0.49 ( 3) link_ALPHA1-3 : angle 2.14574 / 1.39 ( 9) link_ALPHA1-6 : bond 0.00349 / 0.17 ( 2) link_ALPHA1-6 : angle 1.79402 / 1.11 ( 6) link_BETA1-4 : bond 0.00293 / 0.16 ( 16) link_BETA1-4 : angle 1.39313 / 0.86 ( 48) link_NAG-ASN : bond 0.00207 / 0.09 ( 11) link_NAG-ASN : angle 1.48946 / 0.89 ( 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 79 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6637 (mt0) cc_final: 0.6196 (mm-40) REVERT: A 546 MET cc_start: 0.6207 (mpp) cc_final: 0.5702 (mpp) REVERT: B 77 ASN cc_start: 0.7836 (m-40) cc_final: 0.7431 (p0) REVERT: B 285 ASN cc_start: 0.8718 (m-40) cc_final: 0.8393 (t0) REVERT: B 287 MET cc_start: 0.8508 (mmm) cc_final: 0.8275 (tpp) REVERT: B 361 GLU cc_start: 0.8664 (tt0) cc_final: 0.8370 (tp30) REVERT: B 378 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7922 (mttp) REVERT: L 103 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8104 (ttmm) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 1.0967 time to fit residues: 85.6589 Evaluate side-chains 70 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.088137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.061947 restraints weight = 46838.865| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.92 r_work: 0.2737 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 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 = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4000 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= 0.134 Angle : 0.560 6.975 12793 Z= 0.280 Chirality : 0.043 0.205 1482 Planarity : 0.004 0.035 1609 Dihedral : 6.333 53.494 1882 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.26 % Allowed : 10.69 % Favored : 88.05 % 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 are not related in a simple way. whole: -0.46 (0.24), residues: 1128 helix: -0.32 (0.49), residues: 106 sheet: 0.30 (0.25), residues: 382 loop : -0.65 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 271 TYR 0.013 0.001 TYR L 49 PHE 0.019 0.001 PHE H 29 TRP 0.007 0.001 TRP A 188 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 9343) covalent geometry : angle 0.54508 / 0.28 (12679) SS BOND : bond 0.00716 / 0.35 ( 9) SS BOND : angle 0.97896 / 0.59 ( 18) hydrogen bonds : bond 0.03458 / 2.27 ( 313) hydrogen bonds : angle 5.37282 / 3.69 ( 810) link_ALPHA1-3 : bond 0.00903 / 0.47 ( 3) link_ALPHA1-3 : angle 2.11593 / 1.36 ( 9) link_ALPHA1-6 : bond 0.00421 / 0.21 ( 2) link_ALPHA1-6 : angle 1.81113 / 1.09 ( 6) link_BETA1-4 : bond 0.00292 / 0.16 ( 16) link_BETA1-4 : angle 1.39927 / 0.86 ( 48) link_NAG-ASN : bond 0.00226 / 0.11 ( 11) link_NAG-ASN : angle 1.42672 / 0.82 ( 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 74 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6736 (mt0) cc_final: 0.6292 (mm-40) REVERT: A 546 MET cc_start: 0.6222 (mpp) cc_final: 0.5739 (mpp) REVERT: B 77 ASN cc_start: 0.7870 (m-40) cc_final: 0.7447 (p0) REVERT: B 285 ASN cc_start: 0.8732 (m-40) cc_final: 0.8429 (t0) REVERT: B 361 GLU cc_start: 0.8727 (tt0) cc_final: 0.8322 (tp30) REVERT: B 378 LYS cc_start: 0.8318 (mtmm) cc_final: 0.7924 (mttp) REVERT: H 58 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8460 (mt-10) outliers start: 12 outliers final: 9 residues processed: 69 average time/residue: 1.1724 time to fit residues: 87.3731 Evaluate side-chains 69 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 48 MET Chi-restraints excluded: chain L residue 60 ASP 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: 0.0980 chunk 94 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 91 optimal weight: 0.0170 chunk 56 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.062351 restraints weight = 47142.169| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.91 r_work: 0.2744 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 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 = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9384 Z= 0.116 Angle : 0.547 6.737 12793 Z= 0.272 Chirality : 0.043 0.210 1482 Planarity : 0.004 0.058 1609 Dihedral : 6.073 53.345 1882 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.15 % Allowed : 11.01 % Favored : 87.84 % 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 are not related in a simple way. whole: -0.40 (0.24), residues: 1128 helix: -0.21 (0.50), residues: 106 sheet: 0.34 (0.25), residues: 382 loop : -0.61 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 271 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 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9343) covalent geometry : angle 0.53429 / 0.27 (12679) SS BOND : bond 0.00686 / 0.34 ( 9) SS BOND : angle 0.92032 / 0.56 ( 18) hydrogen bonds : bond 0.03284 / 2.16 ( 313) hydrogen bonds : angle 5.27538 / 3.62 ( 810) link_ALPHA1-3 : bond 0.00863 / 0.45 ( 3) link_ALPHA1-3 : angle 1.98156 / 1.29 ( 9) link_ALPHA1-6 : bond 0.00463 / 0.23 ( 2) link_ALPHA1-6 : angle 1.81075 / 1.08 ( 6) link_BETA1-4 : bond 0.00279 / 0.15 ( 16) link_BETA1-4 : angle 1.32542 / 0.82 ( 48) link_NAG-ASN : bond 0.00185 / 0.09 ( 11) link_NAG-ASN : angle 1.32689 / 0.77 ( 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 68 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6798 (mt0) cc_final: 0.6361 (mm-40) REVERT: A 546 MET cc_start: 0.6188 (mpp) cc_final: 0.5714 (mpp) REVERT: B 77 ASN cc_start: 0.7914 (m-40) cc_final: 0.7452 (p0) REVERT: B 285 ASN cc_start: 0.8726 (m-40) cc_final: 0.8430 (t0) REVERT: B 361 GLU cc_start: 0.8737 (tt0) cc_final: 0.8395 (tp30) REVERT: B 378 LYS cc_start: 0.8320 (mtmm) cc_final: 0.7934 (mttp) REVERT: H 58 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8477 (mt-10) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 1.0762 time to fit residues: 73.3175 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 : 0.440 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.061671 restraints weight = 46748.809| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.91 r_work: 0.2774 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 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 = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9384 Z= 0.148 Angle : 0.557 6.953 12793 Z= 0.277 Chirality : 0.043 0.203 1482 Planarity : 0.004 0.058 1609 Dihedral : 5.992 55.605 1882 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.57 % Allowed : 10.80 % Favored : 87.63 % 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 are not related in a simple way. whole: -0.33 (0.24), residues: 1128 helix: -0.17 (0.49), residues: 106 sheet: 0.39 (0.25), residues: 387 loop : -0.58 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 271 TYR 0.013 0.001 TYR B 325 PHE 0.014 0.001 PHE H 29 TRP 0.007 0.001 TRP A 157 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 9343) covalent geometry : angle 0.54264 / 0.27 (12679) SS BOND : bond 0.00576 / 0.28 ( 9) SS BOND : angle 1.01691 / 0.61 ( 18) hydrogen bonds : bond 0.03382 / 2.23 ( 313) hydrogen bonds : angle 5.24492 / 3.59 ( 810) link_ALPHA1-3 : bond 0.00838 / 0.44 ( 3) link_ALPHA1-3 : angle 2.07231 / 1.36 ( 9) link_ALPHA1-6 : bond 0.00473 / 0.24 ( 2) link_ALPHA1-6 : angle 1.80571 / 1.09 ( 6) link_BETA1-4 : bond 0.00291 / 0.15 ( 16) link_BETA1-4 : angle 1.36295 / 0.84 ( 48) link_NAG-ASN : bond 0.00227 / 0.10 ( 11) link_NAG-ASN : angle 1.41942 / 0.83 ( 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 72 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6902 (mt0) cc_final: 0.6449 (mm-40) REVERT: A 271 ARG cc_start: 0.7906 (mtp-110) cc_final: 0.7695 (mtm110) REVERT: A 546 MET cc_start: 0.6156 (mpp) cc_final: 0.5665 (mpp) REVERT: B 285 ASN cc_start: 0.8733 (m-40) cc_final: 0.8461 (t0) REVERT: B 361 GLU cc_start: 0.8738 (tt0) cc_final: 0.8332 (tp30) REVERT: B 378 LYS cc_start: 0.8358 (mtmm) cc_final: 0.7979 (mttp) REVERT: H 58 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8480 (mt-10) outliers start: 15 outliers final: 10 residues processed: 64 average time/residue: 1.0622 time to fit residues: 73.3213 Evaluate side-chains 65 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 270 ILE 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 62 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 48 MET 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: 0.7980 chunk 110 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3308 r_free = 0.3308 target = 0.087627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.061378 restraints weight = 46979.108| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.91 r_work: 0.2769 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 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 = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4383 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= 0.147 Angle : 0.552 6.805 12793 Z= 0.275 Chirality : 0.043 0.207 1482 Planarity : 0.004 0.042 1609 Dihedral : 5.910 56.584 1882 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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 are not related in a simple way. whole: -0.30 (0.24), residues: 1128 helix: -0.14 (0.50), residues: 106 sheet: 0.40 (0.25), residues: 390 loop : -0.55 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 271 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 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9343) covalent geometry : angle 0.53879 / 0.27 (12679) SS BOND : bond 0.00694 / 0.34 ( 9) SS BOND : angle 1.00403 / 0.61 ( 18) hydrogen bonds : bond 0.03376 / 2.23 ( 313) hydrogen bonds : angle 5.21263 / 3.57 ( 810) link_ALPHA1-3 : bond 0.00817 / 0.43 ( 3) link_ALPHA1-3 : angle 1.99672 / 1.31 ( 9) link_ALPHA1-6 : bond 0.00498 / 0.25 ( 2) link_ALPHA1-6 : angle 1.80183 / 1.06 ( 6) link_BETA1-4 : bond 0.00281 / 0.14 ( 16) link_BETA1-4 : angle 1.32383 / 0.82 ( 48) link_NAG-ASN : bond 0.00199 / 0.09 ( 11) link_NAG-ASN : angle 1.38029 / 0.81 ( 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 68 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6939 (mt0) cc_final: 0.6500 (mm-40) REVERT: A 546 MET cc_start: 0.6155 (mpp) cc_final: 0.5678 (mpp) REVERT: B 285 ASN cc_start: 0.8747 (m-40) cc_final: 0.8470 (t0) REVERT: B 361 GLU cc_start: 0.8724 (tt0) cc_final: 0.8324 (tp30) REVERT: B 378 LYS cc_start: 0.8357 (mtmm) cc_final: 0.7984 (mttp) REVERT: H 43 LYS cc_start: 0.8895 (mmtm) cc_final: 0.8554 (mmtt) REVERT: H 58 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8479 (mt-10) outliers start: 9 outliers final: 8 residues processed: 64 average time/residue: 1.0715 time to fit residues: 74.0842 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 : 0.289 ------------------------------------------------------------------------------- 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 H residue 62 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 48 MET 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: 0.0270 chunk 56 optimal weight: 0.6980 chunk 20 optimal weight: 0.0070 chunk 106 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3327 r_free = 0.3327 target = 0.088735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.062598 restraints weight = 46570.260| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.91 r_work: 0.2765 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 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 = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9384 Z= 0.100 Angle : 0.527 5.554 12793 Z= 0.263 Chirality : 0.043 0.212 1482 Planarity : 0.004 0.072 1609 Dihedral : 5.611 55.048 1882 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.73 % Allowed : 11.74 % Favored : 87.53 % 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 are not related in a simple way. whole: -0.17 (0.25), residues: 1128 helix: -0.00 (0.50), residues: 106 sheet: 0.49 (0.25), residues: 388 loop : -0.48 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 271 TYR 0.013 0.001 TYR L 49 PHE 0.016 0.001 PHE H 29 TRP 0.008 0.001 TRP A 188 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 9343) covalent geometry : angle 0.51402 / 0.26 (12679) SS BOND : bond 0.00809 / 0.40 ( 9) SS BOND : angle 0.96622 / 0.59 ( 18) hydrogen bonds : bond 0.03074 / 2.03 ( 313) hydrogen bonds : angle 5.11145 / 3.50 ( 810) link_ALPHA1-3 : bond 0.00827 / 0.43 ( 3) link_ALPHA1-3 : angle 1.87128 / 1.23 ( 9) link_ALPHA1-6 : bond 0.00635 / 0.32 ( 2) link_ALPHA1-6 : angle 1.78602 / 1.04 ( 6) link_BETA1-4 : bond 0.00298 / 0.15 ( 16) link_BETA1-4 : angle 1.28525 / 0.79 ( 48) link_NAG-ASN : bond 0.00158 / 0.08 ( 11) link_NAG-ASN : angle 1.22555 / 0.70 ( 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 65 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6878 (mt0) cc_final: 0.6439 (mm-40) REVERT: A 546 MET cc_start: 0.6154 (mpp) cc_final: 0.5694 (mpp) REVERT: B 285 ASN cc_start: 0.8740 (m-40) cc_final: 0.8444 (t0) REVERT: B 290 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8081 (mtp) REVERT: B 361 GLU cc_start: 0.8742 (tt0) cc_final: 0.8315 (tp30) REVERT: B 378 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7856 (mttp) REVERT: H 43 LYS cc_start: 0.8705 (mmtm) cc_final: 0.8397 (mmtt) REVERT: H 58 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8423 (mt-10) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 1.0730 time to fit residues: 71.8816 Evaluate side-chains 63 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU 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 H residue 93 THR 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: 1.9990 chunk 104 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.061710 restraints weight = 47114.203| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.90 r_work: 0.2760 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 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 = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9384 Z= 0.149 Angle : 0.539 5.766 12793 Z= 0.270 Chirality : 0.043 0.203 1482 Planarity : 0.004 0.048 1609 Dihedral : 5.665 57.033 1882 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.05 % Allowed : 11.53 % 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 are not related in a simple way. whole: -0.18 (0.24), residues: 1128 helix: -0.02 (0.50), residues: 106 sheet: 0.47 (0.25), residues: 390 loop : -0.47 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 271 TYR 0.013 0.001 TYR L 49 PHE 0.013 0.001 PHE H 29 TRP 0.006 0.001 TRP A 188 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 9343) covalent geometry : angle 0.52556 / 0.27 (12679) SS BOND : bond 0.00755 / 0.37 ( 9) SS BOND : angle 1.10605 / 0.67 ( 18) hydrogen bonds : bond 0.03282 / 2.17 ( 313) hydrogen bonds : angle 5.11874 / 3.50 ( 810) link_ALPHA1-3 : bond 0.00784 / 0.41 ( 3) link_ALPHA1-3 : angle 1.96458 / 1.31 ( 9) link_ALPHA1-6 : bond 0.00568 / 0.29 ( 2) link_ALPHA1-6 : angle 1.74088 / 1.03 ( 6) link_BETA1-4 : bond 0.00289 / 0.15 ( 16) link_BETA1-4 : angle 1.31290 / 0.81 ( 48) link_NAG-ASN : bond 0.00184 / 0.09 ( 11) link_NAG-ASN : angle 1.32567 / 0.78 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5497.68 seconds wall clock time: 93 minutes 48.04 seconds (5628.04 seconds total)