Starting phenix.real_space_refine on Sun Jun 15 18:51:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9k_44387/06_2025/9b9k_44387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9k_44387/06_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_44387/06_2025/9b9k_44387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9k_44387/06_2025/9b9k_44387.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9k_44387/06_2025/9b9k_44387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9k_44387/06_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-5710/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: 9.27, per 1000 atoms: 0.53 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: 4.79 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: 1.63 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: 6.96 Time building geometry restraints manager: 5.82 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: 3.270 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: 0.300 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.210 Find NCS groups from input model: 0.210 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.550 ------------------------------------------------------------------------------- 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 : 1.295 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: 3.1355 time to fit residues: 362.3721 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 : 1.331 ------------------------------------------------------------------------------- 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 = 47185.840| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.86 r_work: 0.2779 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 2.91326 ( 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 2.31859 ( 9) hydrogen bonds : bond 0.05250 ( 313) hydrogen bonds : angle 6.67068 ( 810) SS BOND : bond 0.00670 ( 9) SS BOND : angle 1.13587 ( 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 : 1.297 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7376 (pm20) REVERT: A 271 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7712 (ttp80) REVERT: A 546 MET cc_start: 0.6424 (mpp) cc_final: 0.6032 (mpp) REVERT: B 77 ASN cc_start: 0.7551 (m-40) cc_final: 0.7158 (p0) REVERT: B 285 ASN cc_start: 0.8474 (m-40) cc_final: 0.8142 (t0) outliers start: 15 outliers final: 6 residues processed: 71 average time/residue: 2.4080 time to fit residues: 184.1987 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 : 1.308 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 84 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.090092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.063987 restraints weight = 47351.830| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.85 r_work: 0.2747 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 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 = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9384 Z= 0.150 Angle : 0.651 8.841 12793 Z= 0.326 Chirality : 0.047 0.220 1482 Planarity : 0.004 0.038 1609 Dihedral : 9.237 68.107 1884 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.26 % Allowed : 8.28 % Favored : 90.46 % 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: -0.73 (0.23), residues: 1128 helix: -1.21 (0.45), residues: 106 sheet: 0.06 (0.24), residues: 381 loop : -0.64 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.002 0.001 HIS B 301 PHE 0.016 0.001 PHE A 172 TYR 0.015 0.001 TYR A 261 ARG 0.004 0.000 ARG A 423 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 11) link_NAG-ASN : angle 1.62855 ( 33) link_ALPHA1-6 : bond 0.00274 ( 2) link_ALPHA1-6 : angle 1.63509 ( 6) link_BETA1-4 : bond 0.00397 ( 16) link_BETA1-4 : angle 1.90982 ( 48) link_ALPHA1-3 : bond 0.00916 ( 3) link_ALPHA1-3 : angle 2.02172 ( 9) hydrogen bonds : bond 0.04103 ( 313) hydrogen bonds : angle 5.99947 ( 810) SS BOND : bond 0.02032 ( 9) SS BOND : angle 0.95378 ( 18) covalent geometry : bond 0.00337 ( 9343) covalent geometry : angle 0.63337 (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 70 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.370 Fit side-chains REVERT: A 126 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7479 (pm20) REVERT: A 546 MET cc_start: 0.6348 (mpp) cc_final: 0.5766 (mpp) REVERT: B 77 ASN cc_start: 0.7930 (m-40) cc_final: 0.7410 (p0) REVERT: B 285 ASN cc_start: 0.8512 (m-40) cc_final: 0.8140 (t0) REVERT: B 287 MET cc_start: 0.8566 (mmm) cc_final: 0.8308 (tpp) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 2.7327 time to fit residues: 185.3193 Evaluate side-chains 55 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 48 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 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 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.089014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.063227 restraints weight = 47268.324| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.85 r_work: 0.2788 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 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 = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9384 Z= 0.148 Angle : 0.605 7.405 12793 Z= 0.302 Chirality : 0.044 0.200 1482 Planarity : 0.005 0.100 1609 Dihedral : 7.063 59.267 1882 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.36 % Allowed : 8.91 % 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: -0.53 (0.24), residues: 1128 helix: -0.66 (0.48), residues: 106 sheet: 0.16 (0.24), residues: 390 loop : -0.56 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 188 HIS 0.002 0.001 HIS B 301 PHE 0.029 0.001 PHE H 29 TYR 0.015 0.001 TYR L 49 ARG 0.007 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 11) link_NAG-ASN : angle 1.50837 ( 33) link_ALPHA1-6 : bond 0.00343 ( 2) link_ALPHA1-6 : angle 1.77269 ( 6) link_BETA1-4 : bond 0.00321 ( 16) link_BETA1-4 : angle 1.62709 ( 48) link_ALPHA1-3 : bond 0.00984 ( 3) link_ALPHA1-3 : angle 2.34367 ( 9) hydrogen bonds : bond 0.03733 ( 313) hydrogen bonds : angle 5.61965 ( 810) SS BOND : bond 0.00718 ( 9) SS BOND : angle 1.00699 ( 18) covalent geometry : bond 0.00349 ( 9343) covalent geometry : angle 0.58892 (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 74 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.524 Fit side-chains REVERT: A 126 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7531 (pm20) REVERT: A 284 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: A 546 MET cc_start: 0.6156 (mpp) cc_final: 0.5641 (mpp) REVERT: A 578 ASP cc_start: 0.6633 (m-30) cc_final: 0.6196 (m-30) REVERT: B 77 ASN cc_start: 0.7876 (m-40) cc_final: 0.7492 (p0) REVERT: B 285 ASN cc_start: 0.8617 (m-40) cc_final: 0.8310 (t0) outliers start: 13 outliers final: 6 residues processed: 68 average time/residue: 2.6674 time to fit residues: 196.0119 Evaluate side-chains 61 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 1.407 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 77 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 B 141 ASN B 201 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.060264 restraints weight = 47917.078| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.90 r_work: 0.2686 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9384 Z= 0.237 Angle : 0.633 8.106 12793 Z= 0.317 Chirality : 0.045 0.187 1482 Planarity : 0.004 0.036 1609 Dihedral : 7.011 58.250 1882 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.57 % Allowed : 9.96 % Favored : 88.47 % 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: -0.56 (0.24), residues: 1128 helix: -0.55 (0.49), residues: 106 sheet: 0.18 (0.24), residues: 390 loop : -0.65 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 247 HIS 0.003 0.001 HIS B 301 PHE 0.014 0.002 PHE A 172 TYR 0.016 0.002 TYR A 119 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 11) link_NAG-ASN : angle 1.75418 ( 33) link_ALPHA1-6 : bond 0.00230 ( 2) link_ALPHA1-6 : angle 1.78982 ( 6) link_BETA1-4 : bond 0.00326 ( 16) link_BETA1-4 : angle 1.50645 ( 48) link_ALPHA1-3 : bond 0.00978 ( 3) link_ALPHA1-3 : angle 2.40281 ( 9) hydrogen bonds : bond 0.04063 ( 313) hydrogen bonds : angle 5.61723 ( 810) SS BOND : bond 0.00971 ( 9) SS BOND : angle 0.98789 ( 18) covalent geometry : bond 0.00566 ( 9343) covalent geometry : angle 0.61715 (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 73 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 1.542 Fit side-chains REVERT: A 66 GLN cc_start: 0.6748 (mt0) cc_final: 0.6297 (mm-40) REVERT: A 284 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: A 546 MET cc_start: 0.6270 (mpp) cc_final: 0.5750 (mpp) REVERT: B 77 ASN cc_start: 0.7891 (m-40) cc_final: 0.7444 (p0) REVERT: B 150 MET cc_start: 0.8541 (mmt) cc_final: 0.8321 (mtt) REVERT: B 285 ASN cc_start: 0.8734 (m-40) cc_final: 0.8424 (t0) REVERT: B 361 GLU cc_start: 0.8723 (tt0) cc_final: 0.8405 (tp30) REVERT: B 378 LYS cc_start: 0.8327 (mtmm) cc_final: 0.7929 (mttp) REVERT: L 103 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8155 (ttmm) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 3.0929 time to fit residues: 222.6030 Evaluate side-chains 68 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.087669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.061919 restraints weight = 47428.191| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.86 r_work: 0.2759 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9384 Z= 0.126 Angle : 0.563 6.864 12793 Z= 0.282 Chirality : 0.044 0.207 1482 Planarity : 0.004 0.060 1609 Dihedral : 6.474 55.060 1882 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.15 % Allowed : 10.80 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.42 (0.24), residues: 1128 helix: -0.38 (0.50), residues: 106 sheet: 0.30 (0.25), residues: 382 loop : -0.57 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 188 HIS 0.003 0.001 HIS B 301 PHE 0.020 0.001 PHE H 29 TYR 0.014 0.001 TYR L 49 ARG 0.003 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 11) link_NAG-ASN : angle 1.38384 ( 33) link_ALPHA1-6 : bond 0.00413 ( 2) link_ALPHA1-6 : angle 1.84257 ( 6) link_BETA1-4 : bond 0.00278 ( 16) link_BETA1-4 : angle 1.37061 ( 48) link_ALPHA1-3 : bond 0.00915 ( 3) link_ALPHA1-3 : angle 2.05103 ( 9) hydrogen bonds : bond 0.03471 ( 313) hydrogen bonds : angle 5.42546 ( 810) SS BOND : bond 0.00740 ( 9) SS BOND : angle 1.02769 ( 18) covalent geometry : bond 0.00298 ( 9343) covalent geometry : angle 0.54923 (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 73 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.242 Fit side-chains REVERT: A 66 GLN cc_start: 0.6741 (mt0) cc_final: 0.6277 (mm-40) REVERT: A 284 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: A 546 MET cc_start: 0.6155 (mpp) cc_final: 0.5664 (mpp) REVERT: A 578 ASP cc_start: 0.6629 (m-30) cc_final: 0.6345 (m-30) REVERT: B 77 ASN cc_start: 0.7875 (m-40) cc_final: 0.7434 (p0) REVERT: B 285 ASN cc_start: 0.8721 (m-40) cc_final: 0.8398 (t0) REVERT: B 378 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7873 (mttp) REVERT: H 58 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8284 (mt-10) REVERT: L 81 GLU cc_start: 0.9099 (pt0) cc_final: 0.8890 (pm20) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 2.7510 time to fit residues: 200.9452 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 : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain L residue 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: 0.3980 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3308 r_free = 0.3308 target = 0.087552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.061917 restraints weight = 46856.482| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.85 r_work: 0.2747 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 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 = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4135 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= 0.134 Angle : 0.559 7.042 12793 Z= 0.277 Chirality : 0.043 0.204 1482 Planarity : 0.004 0.052 1609 Dihedral : 6.238 56.596 1882 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.05 % Allowed : 11.22 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.36 (0.24), residues: 1128 helix: -0.30 (0.50), residues: 106 sheet: 0.32 (0.25), residues: 382 loop : -0.53 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 188 HIS 0.003 0.001 HIS B 301 PHE 0.013 0.001 PHE H 29 TYR 0.013 0.001 TYR L 49 ARG 0.006 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 11) link_NAG-ASN : angle 1.40190 ( 33) link_ALPHA1-6 : bond 0.00426 ( 2) link_ALPHA1-6 : angle 1.76618 ( 6) link_BETA1-4 : bond 0.00284 ( 16) link_BETA1-4 : angle 1.36830 ( 48) link_ALPHA1-3 : bond 0.00892 ( 3) link_ALPHA1-3 : angle 2.07400 ( 9) hydrogen bonds : bond 0.03385 ( 313) hydrogen bonds : angle 5.31714 ( 810) SS BOND : bond 0.00763 ( 9) SS BOND : angle 1.00366 ( 18) covalent geometry : bond 0.00319 ( 9343) covalent geometry : angle 0.54458 (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 68 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 1.953 Fit side-chains REVERT: A 66 GLN cc_start: 0.6802 (mt0) cc_final: 0.6344 (mm-40) REVERT: A 271 ARG cc_start: 0.7728 (mtp-110) cc_final: 0.7524 (mtm110) REVERT: A 284 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: A 546 MET cc_start: 0.6129 (mpp) cc_final: 0.5647 (mpp) REVERT: A 578 ASP cc_start: 0.6738 (m-30) cc_final: 0.6474 (m-30) REVERT: B 77 ASN cc_start: 0.7830 (m-40) cc_final: 0.7396 (p0) REVERT: B 285 ASN cc_start: 0.8721 (m-40) cc_final: 0.8413 (t0) REVERT: B 361 GLU cc_start: 0.8730 (tt0) cc_final: 0.8286 (tp30) REVERT: B 378 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7856 (mttp) REVERT: H 58 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8421 (mt-10) REVERT: L 103 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8071 (ttmm) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 3.1263 time to fit residues: 218.9405 Evaluate side-chains 66 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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 85 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 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: 0.9980 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.087128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.061179 restraints weight = 47245.740| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.88 r_work: 0.2720 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9384 Z= 0.159 Angle : 0.561 6.969 12793 Z= 0.280 Chirality : 0.043 0.202 1482 Planarity : 0.004 0.041 1609 Dihedral : 6.171 58.743 1882 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.57 % Allowed : 11.11 % 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: -0.33 (0.25), residues: 1128 helix: -0.23 (0.50), residues: 106 sheet: 0.31 (0.25), residues: 384 loop : -0.51 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 188 HIS 0.003 0.001 HIS B 263 PHE 0.015 0.001 PHE H 29 TYR 0.013 0.001 TYR B 325 ARG 0.006 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 11) link_NAG-ASN : angle 1.43830 ( 33) link_ALPHA1-6 : bond 0.00417 ( 2) link_ALPHA1-6 : angle 1.83564 ( 6) link_BETA1-4 : bond 0.00282 ( 16) link_BETA1-4 : angle 1.35815 ( 48) link_ALPHA1-3 : bond 0.00846 ( 3) link_ALPHA1-3 : angle 2.08709 ( 9) hydrogen bonds : bond 0.03453 ( 313) hydrogen bonds : angle 5.29661 ( 810) SS BOND : bond 0.00836 ( 9) SS BOND : angle 1.02398 ( 18) covalent geometry : bond 0.00380 ( 9343) covalent geometry : angle 0.54669 (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 72 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6837 (mt0) cc_final: 0.6387 (mm-40) REVERT: A 271 ARG cc_start: 0.7761 (mtp-110) cc_final: 0.7557 (mtm110) REVERT: A 284 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.7731 (m-80) REVERT: A 546 MET cc_start: 0.6168 (mpp) cc_final: 0.5682 (mpp) REVERT: B 285 ASN cc_start: 0.8728 (m-40) cc_final: 0.8432 (t0) REVERT: B 378 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7870 (mttp) REVERT: H 58 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8407 (mt-10) REVERT: L 103 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8119 (ttmm) outliers start: 15 outliers final: 7 residues processed: 65 average time/residue: 2.7116 time to fit residues: 194.3125 Evaluate side-chains 64 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 85 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.087429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.061277 restraints weight = 47437.997| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.91 r_work: 0.2750 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.003 0.025 9384 Z= 0.137 Angle : 0.549 6.888 12793 Z= 0.273 Chirality : 0.043 0.209 1482 Planarity : 0.004 0.036 1609 Dihedral : 5.999 59.367 1882 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.07 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: -0.24 (0.25), residues: 1128 helix: -0.25 (0.49), residues: 106 sheet: 0.39 (0.25), residues: 390 loop : -0.44 (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 B 301 PHE 0.014 0.001 PHE H 29 TYR 0.013 0.001 TYR L 49 ARG 0.005 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 11) link_NAG-ASN : angle 1.37035 ( 33) link_ALPHA1-6 : bond 0.00506 ( 2) link_ALPHA1-6 : angle 1.78631 ( 6) link_BETA1-4 : bond 0.00280 ( 16) link_BETA1-4 : angle 1.32228 ( 48) link_ALPHA1-3 : bond 0.00825 ( 3) link_ALPHA1-3 : angle 1.98216 ( 9) hydrogen bonds : bond 0.03340 ( 313) hydrogen bonds : angle 5.23156 ( 810) SS BOND : bond 0.00704 ( 9) SS BOND : angle 1.01863 ( 18) covalent geometry : bond 0.00324 ( 9343) covalent geometry : angle 0.53604 (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 65 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 3.712 Fit side-chains REVERT: A 66 GLN cc_start: 0.6922 (mt0) cc_final: 0.6472 (mm-40) REVERT: A 284 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: A 546 MET cc_start: 0.6165 (mpp) cc_final: 0.5680 (mpp) REVERT: B 378 LYS cc_start: 0.8324 (mtmm) cc_final: 0.7938 (mttp) REVERT: H 43 LYS cc_start: 0.8875 (mmtm) cc_final: 0.8526 (mmtt) REVERT: H 58 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8446 (mt-10) REVERT: L 103 LYS cc_start: 0.8430 (ttmm) cc_final: 0.8153 (ttmm) outliers start: 10 outliers final: 8 residues processed: 61 average time/residue: 3.1002 time to fit residues: 206.9932 Evaluate side-chains 62 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 2.356 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 78 optimal weight: 0.0770 overall best weight: 0.4940 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.087918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.061874 restraints weight = 47087.543| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.90 r_work: 0.2762 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 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 = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9384 Z= 0.109 Angle : 0.528 6.029 12793 Z= 0.264 Chirality : 0.043 0.212 1482 Planarity : 0.004 0.087 1609 Dihedral : 5.767 59.223 1882 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.94 % Allowed : 11.32 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1128 helix: -0.13 (0.50), residues: 106 sheet: 0.46 (0.25), residues: 388 loop : -0.40 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 188 HIS 0.003 0.001 HIS B 301 PHE 0.015 0.001 PHE H 29 TYR 0.013 0.001 TYR L 49 ARG 0.012 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 11) link_NAG-ASN : angle 1.26309 ( 33) link_ALPHA1-6 : bond 0.00587 ( 2) link_ALPHA1-6 : angle 1.80003 ( 6) link_BETA1-4 : bond 0.00294 ( 16) link_BETA1-4 : angle 1.29605 ( 48) link_ALPHA1-3 : bond 0.00826 ( 3) link_ALPHA1-3 : angle 1.91108 ( 9) hydrogen bonds : bond 0.03148 ( 313) hydrogen bonds : angle 5.14441 ( 810) SS BOND : bond 0.00642 ( 9) SS BOND : angle 1.00815 ( 18) covalent geometry : bond 0.00256 ( 9343) covalent geometry : angle 0.51518 (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 64 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6905 (mt0) cc_final: 0.6473 (mm-40) REVERT: A 284 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: A 546 MET cc_start: 0.6171 (mpp) cc_final: 0.5773 (mpp) REVERT: B 361 GLU cc_start: 0.8722 (tt0) cc_final: 0.8302 (tp30) REVERT: B 378 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7878 (mttp) REVERT: H 43 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8402 (mmtt) REVERT: H 58 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8401 (mt-10) REVERT: L 85 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8478 (t0) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 3.0614 time to fit residues: 196.6634 Evaluate side-chains 62 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 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: 0.6980 chunk 101 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 chunk 26 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.087483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.061373 restraints weight = 47355.439| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.89 r_work: 0.2756 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9384 Z= 0.141 Angle : 0.548 7.054 12793 Z= 0.273 Chirality : 0.043 0.204 1482 Planarity : 0.004 0.115 1609 Dihedral : 5.769 59.887 1882 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.15 % Allowed : 11.32 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.49), residues: 106 sheet: 0.45 (0.25), residues: 390 loop : -0.38 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 188 HIS 0.003 0.001 HIS B 301 PHE 0.013 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 0.00188 ( 11) link_NAG-ASN : angle 1.34675 ( 33) link_ALPHA1-6 : bond 0.00552 ( 2) link_ALPHA1-6 : angle 1.74624 ( 6) link_BETA1-4 : bond 0.00289 ( 16) link_BETA1-4 : angle 1.31992 ( 48) link_ALPHA1-3 : bond 0.00780 ( 3) link_ALPHA1-3 : angle 1.97313 ( 9) hydrogen bonds : bond 0.03286 ( 313) hydrogen bonds : angle 5.12682 ( 810) SS BOND : bond 0.00784 ( 9) SS BOND : angle 1.18457 ( 18) covalent geometry : bond 0.00337 ( 9343) covalent geometry : angle 0.53398 (12679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13023.30 seconds wall clock time: 230 minutes 12.82 seconds (13812.82 seconds total)