Starting phenix.real_space_refine on Sun May 18 23:55:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9k_44387/05_2025/9b9k_44387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9k_44387/05_2025/9b9k_44387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b9k_44387/05_2025/9b9k_44387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9k_44387/05_2025/9b9k_44387.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9k_44387/05_2025/9b9k_44387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9k_44387/05_2025/9b9k_44387.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17554 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 7800 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 35, 'TRANS': 497} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 5846 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 15, 'TRANS': 361} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1856 Classifications: {'peptide': 120} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1630 Classifications: {'peptide': 112} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.67, per 1000 atoms: 0.49 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: 4.92 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.65 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: 6.45 Time building geometry restraints manager: 5.80 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: 1.970 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: 0.320 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.360 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.085 9384 Z= 0.762 Angle : 1.989 28.613 12793 Z= 1.281 Chirality : 0.112 1.108 1482 Planarity : 0.024 0.311 1609 Dihedral : 16.996 108.551 3869 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.10 % Allowed : 1.57 % Favored : 98.32 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (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 TRP 0.140 0.025 TRP B 247 HIS 0.013 0.004 HIS H 3 PHE 0.068 0.014 PHE A 172 TYR 0.100 0.020 TYR L 31 ARG 0.007 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.02244 ( 11) link_NAG-ASN : angle 4.92400 ( 33) link_ALPHA1-6 : bond 0.03900 ( 2) link_ALPHA1-6 : angle 5.18607 ( 6) link_BETA1-4 : bond 0.02404 ( 16) link_BETA1-4 : angle 3.58677 ( 48) link_ALPHA1-3 : bond 0.03969 ( 3) link_ALPHA1-3 : angle 2.43395 ( 9) hydrogen bonds : bond 0.15494 ( 313) hydrogen bonds : angle 8.08968 ( 810) SS BOND : bond 0.01259 ( 9) SS BOND : angle 2.33430 ( 18) covalent geometry : bond 0.01252 ( 9343) covalent geometry : angle 1.96368 (12679) *********************** 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 : 1.447 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: 3.0659 time to fit residues: 353.8086 Evaluate side-chains 62 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.064831 restraints weight = 47186.111| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.86 r_work: 0.2815 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 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 = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2419 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= 0.199 Angle : 0.792 9.025 12793 Z= 0.401 Chirality : 0.048 0.246 1482 Planarity : 0.005 0.045 1609 Dihedral : 12.858 77.715 1884 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.57 % Allowed : 6.71 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1128 helix: -1.69 (0.42), residues: 106 sheet: 0.05 (0.24), residues: 386 loop : -0.67 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 103 HIS 0.007 0.001 HIS B 301 PHE 0.016 0.002 PHE H 29 TYR 0.018 0.002 TYR L 49 ARG 0.009 0.001 ARG B 155 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 11) link_NAG-ASN : angle 2.91324 ( 33) link_ALPHA1-6 : bond 0.00334 ( 2) link_ALPHA1-6 : angle 1.48929 ( 6) link_BETA1-4 : bond 0.00430 ( 16) link_BETA1-4 : angle 2.49106 ( 48) link_ALPHA1-3 : bond 0.00957 ( 3) link_ALPHA1-3 : angle 2.31861 ( 9) hydrogen bonds : bond 0.05250 ( 313) hydrogen bonds : angle 6.67067 ( 810) SS BOND : bond 0.00670 ( 9) SS BOND : angle 1.13586 ( 18) covalent geometry : bond 0.00470 ( 9343) covalent geometry : angle 0.76235 (12679) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 457 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7313 (pm20) REVERT: A 271 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7652 (ttp80) REVERT: A 546 MET cc_start: 0.6425 (mpp) cc_final: 0.6036 (mpp) REVERT: B 77 ASN cc_start: 0.7577 (m-40) cc_final: 0.7151 (p0) REVERT: B 285 ASN cc_start: 0.8490 (m-40) cc_final: 0.8131 (t0) outliers start: 15 outliers final: 6 residues processed: 71 average time/residue: 2.4418 time to fit residues: 187.1399 Evaluate side-chains 61 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 84 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.090295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.064244 restraints weight = 47353.475| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.87 r_work: 0.2803 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 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 = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9384 Z= 0.141 Angle : 0.641 8.467 12793 Z= 0.320 Chirality : 0.046 0.200 1482 Planarity : 0.004 0.044 1609 Dihedral : 8.704 65.886 1884 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.26 % Allowed : 8.07 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1128 helix: -1.12 (0.46), residues: 106 sheet: 0.08 (0.24), residues: 390 loop : -0.64 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.002 0.001 HIS L 28 PHE 0.015 0.001 PHE A 172 TYR 0.014 0.001 TYR A 261 ARG 0.004 0.000 ARG A 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 11) link_NAG-ASN : angle 1.55939 ( 33) link_ALPHA1-6 : bond 0.00414 ( 2) link_ALPHA1-6 : angle 1.67039 ( 6) link_BETA1-4 : bond 0.00390 ( 16) link_BETA1-4 : angle 1.86255 ( 48) link_ALPHA1-3 : bond 0.01128 ( 3) link_ALPHA1-3 : angle 2.09807 ( 9) hydrogen bonds : bond 0.03982 ( 313) hydrogen bonds : angle 5.91063 ( 810) SS BOND : bond 0.01800 ( 9) SS BOND : angle 1.34115 ( 18) covalent geometry : bond 0.00327 ( 9343) covalent geometry : angle 0.62329 (12679) *********************** 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: 12 poor density : 61 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7438 (pm20) REVERT: A 546 MET cc_start: 0.6315 (mpp) cc_final: 0.5859 (mpp) REVERT: B 77 ASN cc_start: 0.7927 (m-40) cc_final: 0.7396 (p0) REVERT: B 285 ASN cc_start: 0.8496 (m-40) cc_final: 0.8124 (t0) REVERT: B 287 MET cc_start: 0.8508 (mmm) cc_final: 0.8250 (tpp) outliers start: 12 outliers final: 4 residues processed: 66 average time/residue: 2.6463 time to fit residues: 188.1148 Evaluate side-chains 55 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN A 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.089197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.063127 restraints weight = 47377.055| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.90 r_work: 0.2743 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 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 = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3466 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= 0.150 Angle : 0.603 7.280 12793 Z= 0.301 Chirality : 0.044 0.199 1482 Planarity : 0.004 0.085 1609 Dihedral : 6.977 58.784 1882 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.47 % Allowed : 8.81 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1128 helix: -0.65 (0.48), residues: 106 sheet: 0.17 (0.24), residues: 390 loop : -0.54 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 188 HIS 0.002 0.001 HIS H 3 PHE 0.029 0.001 PHE H 29 TYR 0.015 0.001 TYR L 49 ARG 0.003 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 11) link_NAG-ASN : angle 1.56813 ( 33) link_ALPHA1-6 : bond 0.00360 ( 2) link_ALPHA1-6 : angle 1.80135 ( 6) link_BETA1-4 : bond 0.00331 ( 16) link_BETA1-4 : angle 1.62456 ( 48) link_ALPHA1-3 : bond 0.00942 ( 3) link_ALPHA1-3 : angle 2.37993 ( 9) hydrogen bonds : bond 0.03750 ( 313) hydrogen bonds : angle 5.60251 ( 810) SS BOND : bond 0.00572 ( 9) SS BOND : angle 1.06512 ( 18) covalent geometry : bond 0.00355 ( 9343) covalent geometry : angle 0.58618 (12679) *********************** 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 77 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7463 (pm20) REVERT: A 284 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: A 546 MET cc_start: 0.6178 (mpp) cc_final: 0.5656 (mpp) REVERT: A 578 ASP cc_start: 0.6731 (m-30) cc_final: 0.6369 (m-30) REVERT: B 77 ASN cc_start: 0.7889 (m-40) cc_final: 0.7483 (p0) REVERT: B 285 ASN cc_start: 0.8606 (m-40) cc_final: 0.8268 (t0) REVERT: B 361 GLU cc_start: 0.8443 (tt0) cc_final: 0.8191 (tp30) REVERT: B 378 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7885 (mttp) outliers start: 14 outliers final: 7 residues processed: 70 average time/residue: 2.3837 time to fit residues: 179.8811 Evaluate side-chains 65 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 90 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN A 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.088130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.062365 restraints weight = 47369.737| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.86 r_work: 0.2717 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 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 = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9384 Z= 0.146 Angle : 0.577 7.380 12793 Z= 0.287 Chirality : 0.044 0.199 1482 Planarity : 0.004 0.038 1609 Dihedral : 6.574 55.227 1882 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.36 % Allowed : 9.85 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1128 helix: -0.44 (0.49), residues: 106 sheet: 0.24 (0.25), residues: 390 loop : -0.51 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 188 HIS 0.002 0.001 HIS H 3 PHE 0.012 0.001 PHE A 172 TYR 0.013 0.001 TYR L 49 ARG 0.004 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 11) link_NAG-ASN : angle 1.46330 ( 33) link_ALPHA1-6 : bond 0.00376 ( 2) link_ALPHA1-6 : angle 1.80258 ( 6) link_BETA1-4 : bond 0.00355 ( 16) link_BETA1-4 : angle 1.41767 ( 48) link_ALPHA1-3 : bond 0.00958 ( 3) link_ALPHA1-3 : angle 2.14806 ( 9) hydrogen bonds : bond 0.03567 ( 313) hydrogen bonds : angle 5.47112 ( 810) SS BOND : bond 0.00759 ( 9) SS BOND : angle 0.91329 ( 18) covalent geometry : bond 0.00350 ( 9343) covalent geometry : angle 0.56285 (12679) *********************** 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 77 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.292 Fit side-chains REVERT: A 126 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7507 (pm20) REVERT: A 284 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: A 546 MET cc_start: 0.6193 (mpp) cc_final: 0.5682 (mpp) REVERT: A 578 ASP cc_start: 0.6769 (m-30) cc_final: 0.6358 (m-30) REVERT: B 77 ASN cc_start: 0.7952 (m-40) cc_final: 0.7503 (p0) REVERT: B 285 ASN cc_start: 0.8694 (m-40) cc_final: 0.8363 (t0) REVERT: B 287 MET cc_start: 0.8497 (mmm) cc_final: 0.8258 (tpp) REVERT: B 361 GLU cc_start: 0.8647 (tt0) cc_final: 0.8339 (tp30) REVERT: B 378 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7889 (mttp) REVERT: H 43 LYS cc_start: 0.8621 (mmtm) cc_final: 0.8346 (mmtm) REVERT: L 103 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8150 (ttmm) outliers start: 13 outliers final: 7 residues processed: 71 average time/residue: 2.3270 time to fit residues: 178.6304 Evaluate side-chains 69 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 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 104 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN B 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.087768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.062006 restraints weight = 47481.971| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.86 r_work: 0.2761 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 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 = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3971 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 : 0.565 7.065 12793 Z= 0.282 Chirality : 0.043 0.204 1482 Planarity : 0.004 0.076 1609 Dihedral : 6.305 55.124 1882 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.57 % Allowed : 10.48 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1128 helix: -0.30 (0.50), residues: 106 sheet: 0.32 (0.25), residues: 382 loop : -0.52 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 188 HIS 0.004 0.001 HIS B 301 PHE 0.019 0.001 PHE H 29 TYR 0.014 0.001 TYR L 49 ARG 0.007 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 11) link_NAG-ASN : angle 1.44540 ( 33) link_ALPHA1-6 : bond 0.00397 ( 2) link_ALPHA1-6 : angle 1.81864 ( 6) link_BETA1-4 : bond 0.00289 ( 16) link_BETA1-4 : angle 1.41557 ( 48) link_ALPHA1-3 : bond 0.00807 ( 3) link_ALPHA1-3 : angle 2.10665 ( 9) hydrogen bonds : bond 0.03479 ( 313) hydrogen bonds : angle 5.36310 ( 810) SS BOND : bond 0.00720 ( 9) SS BOND : angle 0.99331 ( 18) covalent geometry : bond 0.00353 ( 9343) covalent geometry : angle 0.55050 (12679) *********************** 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: 15 poor density : 59 time to evaluate : 1.358 Fit side-chains REVERT: A 66 GLN cc_start: 0.6676 (mt0) cc_final: 0.6230 (mm-40) REVERT: A 271 ARG cc_start: 0.7785 (mtp-110) cc_final: 0.7533 (mtm110) REVERT: A 284 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: A 546 MET cc_start: 0.6179 (mpp) cc_final: 0.5689 (mpp) REVERT: B 77 ASN cc_start: 0.7864 (m-40) cc_final: 0.7430 (p0) REVERT: B 150 MET cc_start: 0.8456 (mmt) cc_final: 0.8252 (mtt) REVERT: B 361 GLU cc_start: 0.8717 (tt0) cc_final: 0.8368 (tp30) REVERT: B 378 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7843 (mttp) REVERT: H 58 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8509 (mt-10) outliers start: 15 outliers final: 8 residues processed: 67 average time/residue: 2.5868 time to fit residues: 186.5636 Evaluate side-chains 67 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 chunk 49 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.062300 restraints weight = 46942.710| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.88 r_work: 0.2780 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 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 = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4132 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 : 0.540 6.813 12793 Z= 0.269 Chirality : 0.043 0.211 1482 Planarity : 0.003 0.039 1609 Dihedral : 6.022 55.095 1882 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.47 % Allowed : 10.59 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1128 helix: -0.17 (0.50), residues: 106 sheet: 0.40 (0.25), residues: 387 loop : -0.44 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 188 HIS 0.002 0.001 HIS A 587 PHE 0.013 0.001 PHE H 29 TYR 0.013 0.001 TYR L 49 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 11) link_NAG-ASN : angle 1.30762 ( 33) link_ALPHA1-6 : bond 0.00486 ( 2) link_ALPHA1-6 : angle 1.82121 ( 6) link_BETA1-4 : bond 0.00287 ( 16) link_BETA1-4 : angle 1.30587 ( 48) link_ALPHA1-3 : bond 0.00876 ( 3) link_ALPHA1-3 : angle 1.97168 ( 9) hydrogen bonds : bond 0.03243 ( 313) hydrogen bonds : angle 5.26282 ( 810) SS BOND : bond 0.00640 ( 9) SS BOND : angle 0.95110 ( 18) covalent geometry : bond 0.00273 ( 9343) covalent geometry : angle 0.52700 (12679) *********************** 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 72 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6842 (mt0) cc_final: 0.6397 (mm-40) REVERT: A 501 PHE cc_start: 0.7303 (m-80) cc_final: 0.7035 (m-80) REVERT: A 546 MET cc_start: 0.6181 (mpp) cc_final: 0.5689 (mpp) REVERT: A 578 ASP cc_start: 0.6826 (m-30) cc_final: 0.6575 (m-30) REVERT: B 77 ASN cc_start: 0.7892 (m-40) cc_final: 0.7433 (p0) REVERT: B 287 MET cc_start: 0.8469 (mmm) cc_final: 0.8259 (tpp) REVERT: B 361 GLU cc_start: 0.8620 (tt0) cc_final: 0.8290 (tp30) REVERT: B 378 LYS cc_start: 0.8303 (mtmm) cc_final: 0.7916 (mttp) REVERT: H 58 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8506 (mt-10) REVERT: L 103 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8101 (ttmm) outliers start: 14 outliers final: 9 residues processed: 65 average time/residue: 2.3993 time to fit residues: 168.8549 Evaluate side-chains 66 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 62 SER 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 85 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.061284 restraints weight = 47240.510| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.88 r_work: 0.2725 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 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 = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4220 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= 0.172 Angle : 0.562 7.060 12793 Z= 0.280 Chirality : 0.044 0.201 1482 Planarity : 0.004 0.068 1609 Dihedral : 6.076 58.198 1882 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.68 % Allowed : 11.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1128 helix: -0.16 (0.50), residues: 106 sheet: 0.40 (0.25), residues: 389 loop : -0.43 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 157 HIS 0.003 0.001 HIS B 263 PHE 0.015 0.001 PHE H 29 TYR 0.014 0.001 TYR B 325 ARG 0.008 0.001 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 11) link_NAG-ASN : angle 1.46068 ( 33) link_ALPHA1-6 : bond 0.00418 ( 2) link_ALPHA1-6 : angle 1.79798 ( 6) link_BETA1-4 : bond 0.00271 ( 16) link_BETA1-4 : angle 1.36820 ( 48) link_ALPHA1-3 : bond 0.00848 ( 3) link_ALPHA1-3 : angle 2.12158 ( 9) hydrogen bonds : bond 0.03481 ( 313) hydrogen bonds : angle 5.27301 ( 810) SS BOND : bond 0.00805 ( 9) SS BOND : angle 0.99569 ( 18) covalent geometry : bond 0.00415 ( 9343) covalent geometry : angle 0.54774 (12679) *********************** 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 74 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 1.482 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6875 (mt0) cc_final: 0.6414 (mm-40) REVERT: A 284 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: A 546 MET cc_start: 0.6136 (mpp) cc_final: 0.5639 (mpp) REVERT: B 361 GLU cc_start: 0.8739 (tt0) cc_final: 0.8326 (tp30) REVERT: B 378 LYS cc_start: 0.8297 (mtmm) cc_final: 0.7895 (mttp) REVERT: H 43 LYS cc_start: 0.8726 (mmtm) cc_final: 0.8359 (mmtt) REVERT: H 58 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8515 (mt-10) outliers start: 16 outliers final: 9 residues processed: 67 average time/residue: 2.4245 time to fit residues: 175.5784 Evaluate side-chains 66 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain 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 85 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 0.0170 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.061615 restraints weight = 47304.560| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.86 r_work: 0.2755 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9384 Z= 0.148 Angle : 0.560 6.916 12793 Z= 0.278 Chirality : 0.043 0.204 1482 Planarity : 0.004 0.107 1609 Dihedral : 6.026 58.322 1882 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.47 % Allowed : 11.32 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1128 helix: -0.17 (0.49), residues: 106 sheet: 0.43 (0.25), residues: 389 loop : -0.42 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 188 HIS 0.003 0.001 HIS A 587 PHE 0.014 0.001 PHE H 29 TYR 0.013 0.001 TYR L 49 ARG 0.017 0.001 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 11) link_NAG-ASN : angle 1.42109 ( 33) link_ALPHA1-6 : bond 0.00467 ( 2) link_ALPHA1-6 : angle 1.81240 ( 6) link_BETA1-4 : bond 0.00278 ( 16) link_BETA1-4 : angle 1.34296 ( 48) link_ALPHA1-3 : bond 0.00804 ( 3) link_ALPHA1-3 : angle 2.02617 ( 9) hydrogen bonds : bond 0.03398 ( 313) hydrogen bonds : angle 5.25575 ( 810) SS BOND : bond 0.00666 ( 9) SS BOND : angle 0.95422 ( 18) covalent geometry : bond 0.00352 ( 9343) covalent geometry : angle 0.54681 (12679) *********************** 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 70 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 1.416 Fit side-chains REVERT: A 66 GLN cc_start: 0.6894 (mt0) cc_final: 0.6448 (mm-40) REVERT: A 284 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: A 546 MET cc_start: 0.6154 (mpp) cc_final: 0.5671 (mpp) REVERT: B 361 GLU cc_start: 0.8761 (tt0) cc_final: 0.8341 (tp30) REVERT: B 378 LYS cc_start: 0.8310 (mtmm) cc_final: 0.7916 (mttp) REVERT: H 58 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8510 (mt-10) REVERT: L 103 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8169 (ttmm) outliers start: 14 outliers final: 9 residues processed: 62 average time/residue: 2.4782 time to fit residues: 165.7868 Evaluate side-chains 66 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain 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 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 103 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 0.0030 chunk 94 optimal weight: 0.3980 chunk 78 optimal weight: 0.3980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.061940 restraints weight = 47080.930| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.89 r_work: 0.2748 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 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 = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9384 Z= 0.118 Angle : 0.548 6.742 12793 Z= 0.272 Chirality : 0.043 0.208 1482 Planarity : 0.004 0.116 1609 Dihedral : 5.920 58.030 1882 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.15 % Allowed : 11.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1128 helix: -0.12 (0.50), residues: 106 sheet: 0.48 (0.25), residues: 388 loop : -0.39 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 188 HIS 0.002 0.001 HIS A 587 PHE 0.015 0.001 PHE H 29 TYR 0.013 0.001 TYR L 49 ARG 0.018 0.001 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 11) link_NAG-ASN : angle 1.34918 ( 33) link_ALPHA1-6 : bond 0.00523 ( 2) link_ALPHA1-6 : angle 1.81318 ( 6) link_BETA1-4 : bond 0.00278 ( 16) link_BETA1-4 : angle 1.32459 ( 48) link_ALPHA1-3 : bond 0.00783 ( 3) link_ALPHA1-3 : angle 1.94124 ( 9) hydrogen bonds : bond 0.03258 ( 313) hydrogen bonds : angle 5.22005 ( 810) SS BOND : bond 0.00875 ( 9) SS BOND : angle 1.10373 ( 18) covalent geometry : bond 0.00278 ( 9343) covalent geometry : angle 0.53407 (12679) ********************** 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 69 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6848 (mt0) cc_final: 0.6404 (mm-40) REVERT: A 546 MET cc_start: 0.6139 (mpp) cc_final: 0.5673 (mpp) REVERT: B 361 GLU cc_start: 0.8746 (tt0) cc_final: 0.8331 (tp30) REVERT: B 378 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7874 (mttp) REVERT: H 58 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8490 (mt-10) REVERT: L 103 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8130 (ttmm) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 2.4227 time to fit residues: 167.6667 Evaluate side-chains 64 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 31 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.061578 restraints weight = 47066.546| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.85 r_work: 0.2740 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9384 Z= 0.149 Angle : 0.551 5.858 12793 Z= 0.276 Chirality : 0.043 0.206 1482 Planarity : 0.004 0.112 1609 Dihedral : 5.906 58.891 1882 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1128 helix: -0.12 (0.49), residues: 106 sheet: 0.44 (0.25), residues: 390 loop : -0.37 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 188 HIS 0.003 0.001 HIS A 587 PHE 0.014 0.001 PHE H 29 TYR 0.013 0.001 TYR L 49 ARG 0.017 0.001 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 11) link_NAG-ASN : angle 1.37424 ( 33) link_ALPHA1-6 : bond 0.00504 ( 2) link_ALPHA1-6 : angle 1.78895 ( 6) link_BETA1-4 : bond 0.00285 ( 16) link_BETA1-4 : angle 1.32029 ( 48) link_ALPHA1-3 : bond 0.00793 ( 3) link_ALPHA1-3 : angle 2.00997 ( 9) hydrogen bonds : bond 0.03343 ( 313) hydrogen bonds : angle 5.20755 ( 810) SS BOND : bond 0.00772 ( 9) SS BOND : angle 1.06974 ( 18) covalent geometry : bond 0.00356 ( 9343) covalent geometry : angle 0.53703 (12679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11262.33 seconds wall clock time: 193 minutes 29.06 seconds (11609.06 seconds total)