Starting phenix.real_space_refine on Wed Jun 3 15:07:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9upr_64401/06_2026/9upr_64401.cif Found real_map, /net/cci-nas-00/data/ceres_data/9upr_64401/06_2026/9upr_64401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9upr_64401/06_2026/9upr_64401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9upr_64401/06_2026/9upr_64401.map" model { file = "/net/cci-nas-00/data/ceres_data/9upr_64401/06_2026/9upr_64401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9upr_64401/06_2026/9upr_64401.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 644 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 3824 2.51 5 N 993 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6014 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1652 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "B" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1455 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 1 Chain: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 877 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "F" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1946 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 14, 'TRANS': 225} Chain breaks: 5 Chain: "C" 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: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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 Time building chain proxies: 1.91, per 1000 atoms: 0.32 Number of scatterers: 6014 At special positions: 0 Unit cell: (71.07, 86.94, 126.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1176 8.00 N 993 7.00 C 3824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN F 165 " " NAG F 401 " - " ASN F 122 " " NAG F 402 " - " ASN F 61 " " NAG F 403 " - " ASN F 234 " " NAG F 404 " - " ASN F 282 " Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 371.3 milliseconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 14 sheets defined 4.6% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.568A pdb=" N LEU A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.717A pdb=" N THR B 90 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.590A pdb=" N GLY B 167 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA B 168 " --> pdb=" O ASN B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 164 through 168' Processing helix chain 'F' and resid 294 through 303 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.668A pdb=" N VAL A 19 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.605A pdb=" N LEU A 33 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 118 removed outlier: 3.943A pdb=" N VAL A 133 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR A 173 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 154 removed outlier: 3.786A pdb=" N LYS A 145 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 197 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 147 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 195 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.871A pdb=" N MET B 34 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 52 " --> pdb=" O ASN B 56 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.897A pdb=" N GLY B 149 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP B 154 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.892A pdb=" N ILE E 78 " --> pdb=" O CYS E 22 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP E 72 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.642A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET E 34 " --> pdb=" O THR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 27 through 30 removed outlier: 3.739A pdb=" N ALA F 27 " --> pdb=" O TRP F 64 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR F 265 " --> pdb=" O PHE F 65 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA F 264 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE F 95 " --> pdb=" O ALA F 264 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN F 188 " --> pdb=" O GLU F 96 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS F 187 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE F 210 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL F 227 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N HIS F 207 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N LEU F 223 " --> pdb=" O HIS F 207 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL F 36 " --> pdb=" O LEU F 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 48 through 55 removed outlier: 4.081A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 84 through 85 removed outlier: 4.065A pdb=" N GLY F 103 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL F 126 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL F 171 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE F 128 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU F 169 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL F 130 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU F 132 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASN F 165 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLN F 134 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA F 163 " --> pdb=" O GLN F 134 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 534 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: 0.86 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1899 1.34 - 1.46: 1537 1.46 - 1.58: 2694 1.58 - 1.70: 0 1.70 - 1.81: 28 Bond restraints: 6158 Sorted by residual: bond pdb=" C1 NAG F 403 " pdb=" O5 NAG F 403 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1 NAG F 401 " pdb=" O5 NAG F 401 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" C1 NAG F 402 " pdb=" O5 NAG F 402 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.24e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" CA ASN A 210 " pdb=" CB ASN A 210 " ideal model delta sigma weight residual 1.535 1.562 -0.027 1.93e-02 2.68e+03 1.96e+00 ... (remaining 6153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 8171 1.79 - 3.59: 158 3.59 - 5.38: 32 5.38 - 7.17: 3 7.17 - 8.97: 3 Bond angle restraints: 8367 Sorted by residual: angle pdb=" C PHE F 32 " pdb=" CA PHE F 32 " pdb=" CB PHE F 32 " ideal model delta sigma weight residual 116.54 110.22 6.32 1.15e+00 7.56e-01 3.02e+01 angle pdb=" CB LYS A 169 " pdb=" CG LYS A 169 " pdb=" CD LYS A 169 " ideal model delta sigma weight residual 111.30 120.27 -8.97 2.30e+00 1.89e-01 1.52e+01 angle pdb=" C SER F 172 " pdb=" N GLN F 173 " pdb=" CA GLN F 173 " ideal model delta sigma weight residual 120.49 125.19 -4.70 1.42e+00 4.96e-01 1.10e+01 angle pdb=" CB LYS E 64 " pdb=" CG LYS E 64 " pdb=" CD LYS E 64 " ideal model delta sigma weight residual 111.30 118.54 -7.24 2.30e+00 1.89e-01 9.92e+00 angle pdb=" CA PHE F 32 " pdb=" C PHE F 32 " pdb=" N THR F 33 " ideal model delta sigma weight residual 119.52 117.04 2.48 7.90e-01 1.60e+00 9.83e+00 ... (remaining 8362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 3360 16.18 - 32.36: 244 32.36 - 48.55: 76 48.55 - 64.73: 26 64.73 - 80.91: 5 Dihedral angle restraints: 3711 sinusoidal: 1505 harmonic: 2206 Sorted by residual: dihedral pdb=" CA ASN F 122 " pdb=" C ASN F 122 " pdb=" N ALA F 123 " pdb=" CA ALA F 123 " ideal model delta harmonic sigma weight residual -180.00 -159.16 -20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CG ARG E 114 " pdb=" CD ARG E 114 " pdb=" NE ARG E 114 " pdb=" CZ ARG E 114 " ideal model delta sinusoidal sigma weight residual -90.00 -40.36 -49.64 2 1.50e+01 4.44e-03 1.24e+01 dihedral pdb=" CA ASP F 294 " pdb=" CB ASP F 294 " pdb=" CG ASP F 294 " pdb=" OD1 ASP F 294 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 3708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 761 0.049 - 0.098: 125 0.098 - 0.147: 54 0.147 - 0.195: 0 0.195 - 0.244: 3 Chirality restraints: 943 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN F 165 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C1 NAG F 403 " pdb=" ND2 ASN F 234 " pdb=" C2 NAG F 403 " pdb=" O5 NAG F 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ASN F 234 " pdb=" N ASN F 234 " pdb=" C ASN F 234 " pdb=" CB ASN F 234 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 940 not shown) Planarity restraints: 1071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 158 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO B 159 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 114 " -0.108 9.50e-02 1.11e+02 4.86e-02 1.90e+00 pdb=" NE ARG E 114 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG E 114 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 114 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG E 114 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 282 " -0.013 2.00e-02 2.50e+03 1.18e-02 1.73e+00 pdb=" CG ASN F 282 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN F 282 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN F 282 " 0.014 2.00e-02 2.50e+03 pdb=" C1 NAG F 404 " -0.014 2.00e-02 2.50e+03 ... (remaining 1068 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 263 2.71 - 3.26: 5406 3.26 - 3.81: 8806 3.81 - 4.35: 10595 4.35 - 4.90: 19336 Nonbonded interactions: 44406 Sorted by model distance: nonbonded pdb=" N GLU E 88 " pdb=" OE1 GLU E 88 " model vdw 2.167 3.120 nonbonded pdb=" O CYS E 22 " pdb=" OG1 THR E 77 " model vdw 2.210 3.040 nonbonded pdb=" N GLU A 81 " pdb=" OE1 GLU A 81 " model vdw 2.216 3.120 nonbonded pdb=" OD2 ASP E 72 " pdb=" NZ LYS E 75 " model vdw 2.237 3.120 nonbonded pdb=" N GLU F 224 " pdb=" OE1 GLU F 224 " model vdw 2.242 3.120 ... (remaining 44401 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.950 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 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 : 0.003 0.067 6170 Z= 0.159 Angle : 0.653 8.966 8397 Z= 0.332 Chirality : 0.044 0.244 943 Planarity : 0.004 0.054 1066 Dihedral : 13.452 80.912 2281 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 2.59 % Allowed : 18.75 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.32), residues: 744 helix: 1.18 (1.12), residues: 23 sheet: 0.77 (0.31), residues: 318 loop : -0.69 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 114 TYR 0.017 0.001 TYR A 186 PHE 0.010 0.001 PHE F 168 TRP 0.005 0.001 TRP B 164 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 6158) covalent geometry : angle 0.62102 / 0.33 ( 8367) SS BOND : bond 0.00243 / 0.11 ( 6) SS BOND : angle 0.64763 / 0.36 ( 12) hydrogen bonds : bond 0.28213 / 19.21 ( 199) hydrogen bonds : angle 9.32424 / 6.20 ( 534) link_BETA1-4 : bond 0.00623 / 0.33 ( 1) link_BETA1-4 : angle 1.21786 / 0.70 ( 3) link_NAG-ASN : bond 0.01720 / 0.85 ( 5) link_NAG-ASN : angle 4.80333 / 2.85 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8593 (ttt-90) cc_final: 0.8221 (tmt-80) REVERT: E 4 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6353 (pt) REVERT: E 64 LYS cc_start: 0.8568 (mmmm) cc_final: 0.7771 (mmmm) REVERT: E 82 MET cc_start: 0.8771 (tpp) cc_final: 0.8516 (mmm) REVERT: F 191 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8337 (mp0) REVERT: F 218 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8492 (pm20) outliers start: 17 outliers final: 15 residues processed: 84 average time/residue: 0.7525 time to fit residues: 65.5423 Evaluate side-chains 80 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 245 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 294 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.0370 chunk 74 optimal weight: 10.0000 overall best weight: 2.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.077417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.050836 restraints weight = 16714.598| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.87 r_work: 0.2698 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 6170 Z= 0.305 Angle : 0.732 10.846 8397 Z= 0.374 Chirality : 0.048 0.257 943 Planarity : 0.005 0.041 1066 Dihedral : 7.869 59.406 978 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.11 % Favored : 94.76 % Rotamer: Outliers : 5.34 % Allowed : 13.57 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.31), residues: 744 helix: 1.37 (1.03), residues: 25 sheet: 0.68 (0.30), residues: 325 loop : -0.89 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 114 TYR 0.015 0.002 TYR B 94 PHE 0.019 0.002 PHE B 156 TRP 0.012 0.001 TRP B 164 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.30 ( 6158) covalent geometry : angle 0.69633 / 0.37 ( 8367) SS BOND : bond 0.00514 / 0.26 ( 6) SS BOND : angle 1.36749 / 0.75 ( 12) hydrogen bonds : bond 0.05086 / 3.49 ( 199) hydrogen bonds : angle 6.43711 / 4.27 ( 534) link_BETA1-4 : bond 0.00621 / 0.33 ( 1) link_BETA1-4 : angle 1.30314 / 0.69 ( 3) link_NAG-ASN : bond 0.01553 / 0.73 ( 5) link_NAG-ASN : angle 5.22120 / 3.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 61 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8443 (ttmm) REVERT: A 192 TYR cc_start: 0.7802 (m-80) cc_final: 0.7253 (m-80) REVERT: A 211 ARG cc_start: 0.8705 (mtp-110) cc_final: 0.8427 (mpp80) REVERT: A 213 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7288 (pp20) REVERT: E 64 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8295 (mmmm) REVERT: F 218 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8296 (pm20) outliers start: 35 outliers final: 15 residues processed: 91 average time/residue: 0.7052 time to fit residues: 66.6353 Evaluate side-chains 76 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 245 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 44 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.078107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.052091 restraints weight = 16330.715| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.81 r_work: 0.2732 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6170 Z= 0.155 Angle : 0.629 9.061 8397 Z= 0.315 Chirality : 0.044 0.248 943 Planarity : 0.004 0.035 1066 Dihedral : 6.942 57.542 967 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.76 % Favored : 96.10 % Rotamer: Outliers : 4.42 % Allowed : 14.63 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.31), residues: 744 helix: 1.60 (1.04), residues: 25 sheet: 1.00 (0.31), residues: 307 loop : -0.95 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 114 TYR 0.014 0.001 TYR B 94 PHE 0.013 0.001 PHE B 156 TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 6158) covalent geometry : angle 0.59505 / 0.31 ( 8367) SS BOND : bond 0.00363 / 0.19 ( 6) SS BOND : angle 0.86205 / 0.49 ( 12) hydrogen bonds : bond 0.03715 / 2.58 ( 199) hydrogen bonds : angle 5.87818 / 3.92 ( 534) link_BETA1-4 : bond 0.00406 / 0.21 ( 1) link_BETA1-4 : angle 1.36307 / 0.71 ( 3) link_NAG-ASN : bond 0.01489 / 0.72 ( 5) link_NAG-ASN : angle 4.76081 / 2.73 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8792 (ttmm) REVERT: A 108 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.7237 (ppp80) REVERT: A 142 ARG cc_start: 0.8798 (ttt-90) cc_final: 0.8373 (tmt-80) REVERT: A 192 TYR cc_start: 0.7992 (m-80) cc_final: 0.7395 (m-80) REVERT: A 211 ARG cc_start: 0.8684 (mtp-110) cc_final: 0.8401 (mtp180) REVERT: E 64 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8329 (mmmm) REVERT: F 218 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8275 (pm20) outliers start: 29 outliers final: 16 residues processed: 88 average time/residue: 0.6715 time to fit residues: 61.3324 Evaluate side-chains 76 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 245 HIS Chi-restraints excluded: chain F residue 293 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.077651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051367 restraints weight = 16522.858| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.80 r_work: 0.2718 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6170 Z= 0.186 Angle : 0.641 9.041 8397 Z= 0.323 Chirality : 0.045 0.246 943 Planarity : 0.004 0.039 1066 Dihedral : 6.656 55.771 965 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.24 % Favored : 94.62 % Rotamer: Outliers : 4.88 % Allowed : 14.79 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.31), residues: 744 helix: 1.67 (1.05), residues: 25 sheet: 0.92 (0.31), residues: 310 loop : -0.96 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 114 TYR 0.015 0.001 TYR B 94 PHE 0.015 0.001 PHE B 156 TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 ( 6158) covalent geometry : angle 0.60835 / 0.32 ( 8367) SS BOND : bond 0.00439 / 0.23 ( 6) SS BOND : angle 0.97990 / 0.55 ( 12) hydrogen bonds : bond 0.03570 / 2.50 ( 199) hydrogen bonds : angle 5.64473 / 3.77 ( 534) link_BETA1-4 : bond 0.00346 / 0.18 ( 1) link_BETA1-4 : angle 1.41793 / 0.73 ( 3) link_NAG-ASN : bond 0.01353 / 0.65 ( 5) link_NAG-ASN : angle 4.75345 / 2.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8754 (ttmm) REVERT: A 108 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7267 (ppp80) REVERT: A 192 TYR cc_start: 0.8095 (m-80) cc_final: 0.7454 (m-80) REVERT: A 211 ARG cc_start: 0.8768 (mtp-110) cc_final: 0.8436 (mtp180) REVERT: A 213 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7464 (pp20) REVERT: B 72 ASP cc_start: 0.8415 (t0) cc_final: 0.8127 (t70) REVERT: E 64 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8371 (mmmm) outliers start: 32 outliers final: 18 residues processed: 86 average time/residue: 0.6629 time to fit residues: 59.3899 Evaluate side-chains 78 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 245 HIS Chi-restraints excluded: chain F residue 293 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.077601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.051080 restraints weight = 16753.849| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.84 r_work: 0.2717 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6170 Z= 0.177 Angle : 0.639 9.667 8397 Z= 0.319 Chirality : 0.044 0.245 943 Planarity : 0.004 0.036 1066 Dihedral : 6.326 53.435 962 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 5.03 % Allowed : 14.63 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.31), residues: 744 helix: 1.86 (1.08), residues: 25 sheet: 0.79 (0.31), residues: 316 loop : -0.95 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 114 TYR 0.015 0.001 TYR B 94 PHE 0.014 0.001 PHE B 156 TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 6158) covalent geometry : angle 0.60674 / 0.31 ( 8367) SS BOND : bond 0.00393 / 0.21 ( 6) SS BOND : angle 0.95199 / 0.53 ( 12) hydrogen bonds : bond 0.03389 / 2.38 ( 199) hydrogen bonds : angle 5.53954 / 3.72 ( 534) link_BETA1-4 : bond 0.00412 / 0.22 ( 1) link_BETA1-4 : angle 1.46734 / 0.76 ( 3) link_NAG-ASN : bond 0.01262 / 0.60 ( 5) link_NAG-ASN : angle 4.68725 / 2.56 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8722 (ttmm) REVERT: A 108 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7310 (ppp80) REVERT: A 142 ARG cc_start: 0.8885 (ttt-90) cc_final: 0.8486 (tmt-80) REVERT: A 192 TYR cc_start: 0.8128 (m-80) cc_final: 0.7439 (m-80) REVERT: A 211 ARG cc_start: 0.8815 (mtp-110) cc_final: 0.8528 (mtp180) REVERT: A 213 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7557 (pp20) REVERT: B 72 ASP cc_start: 0.8461 (t0) cc_final: 0.8130 (t70) REVERT: B 115 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8284 (p) REVERT: E 64 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8401 (mmmm) REVERT: E 82 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8393 (tpp) REVERT: F 191 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8794 (mp0) REVERT: F 218 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8299 (pm20) outliers start: 33 outliers final: 18 residues processed: 86 average time/residue: 0.6959 time to fit residues: 62.1066 Evaluate side-chains 79 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 245 HIS Chi-restraints excluded: chain F residue 293 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 10.0000 chunk 33 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.078720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.052636 restraints weight = 16359.779| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.77 r_work: 0.2754 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6170 Z= 0.113 Angle : 0.610 10.667 8397 Z= 0.300 Chirality : 0.044 0.238 943 Planarity : 0.004 0.035 1066 Dihedral : 8.272 176.935 962 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 4.57 % Allowed : 15.70 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.32), residues: 744 helix: 1.91 (1.09), residues: 25 sheet: 0.89 (0.31), residues: 319 loop : -0.84 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 19 TYR 0.013 0.001 TYR B 94 PHE 0.009 0.001 PHE F 168 TRP 0.008 0.001 TRP B 47 HIS 0.003 0.000 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 6158) covalent geometry : angle 0.57761 / 0.29 ( 8367) SS BOND : bond 0.00300 / 0.15 ( 6) SS BOND : angle 0.73381 / 0.41 ( 12) hydrogen bonds : bond 0.02890 / 1.99 ( 199) hydrogen bonds : angle 5.34901 / 3.61 ( 534) link_BETA1-4 : bond 0.00478 / 0.25 ( 1) link_BETA1-4 : angle 1.43242 / 0.73 ( 3) link_NAG-ASN : bond 0.01222 / 0.59 ( 5) link_NAG-ASN : angle 4.62651 / 2.45 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8602 (m-30) REVERT: A 107 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8717 (ttmm) REVERT: A 108 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7374 (ppp80) REVERT: A 124 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8443 (mm-40) REVERT: A 192 TYR cc_start: 0.8102 (m-80) cc_final: 0.7475 (m-80) REVERT: A 213 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7595 (pp20) REVERT: B 72 ASP cc_start: 0.8381 (t0) cc_final: 0.8073 (t70) REVERT: B 115 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8244 (p) REVERT: E 64 LYS cc_start: 0.8780 (mmmm) cc_final: 0.8424 (mmmm) outliers start: 30 outliers final: 17 residues processed: 87 average time/residue: 0.7200 time to fit residues: 64.9653 Evaluate side-chains 78 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 245 HIS Chi-restraints excluded: chain F residue 293 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 43 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 0.0670 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.077862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.051664 restraints weight = 16615.686| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.79 r_work: 0.2727 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6170 Z= 0.158 Angle : 0.638 10.262 8397 Z= 0.317 Chirality : 0.044 0.238 943 Planarity : 0.004 0.039 1066 Dihedral : 8.207 179.303 962 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 4.73 % Allowed : 16.16 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.31), residues: 744 helix: 1.85 (1.12), residues: 25 sheet: 0.96 (0.31), residues: 313 loop : -0.93 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 114 TYR 0.015 0.001 TYR B 94 PHE 0.012 0.001 PHE B 156 TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 6158) covalent geometry : angle 0.60646 / 0.31 ( 8367) SS BOND : bond 0.00366 / 0.20 ( 6) SS BOND : angle 0.90566 / 0.50 ( 12) hydrogen bonds : bond 0.03203 / 2.23 ( 199) hydrogen bonds : angle 5.36980 / 3.62 ( 534) link_BETA1-4 : bond 0.00389 / 0.20 ( 1) link_BETA1-4 : angle 1.42122 / 0.73 ( 3) link_NAG-ASN : bond 0.01153 / 0.55 ( 5) link_NAG-ASN : angle 4.64315 / 2.47 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8584 (m-30) REVERT: A 81 GLU cc_start: 0.8846 (pm20) cc_final: 0.8382 (pm20) REVERT: A 107 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8694 (ttmm) REVERT: A 108 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7344 (ppp80) REVERT: A 142 ARG cc_start: 0.8857 (ttt-90) cc_final: 0.8490 (ttp80) REVERT: A 192 TYR cc_start: 0.8160 (m-80) cc_final: 0.7563 (m-80) REVERT: A 213 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.6885 (mm-30) REVERT: B 72 ASP cc_start: 0.8450 (t0) cc_final: 0.8117 (t0) REVERT: B 115 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8279 (p) REVERT: E 64 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8542 (mmmm) REVERT: F 218 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8413 (pm20) outliers start: 31 outliers final: 19 residues processed: 87 average time/residue: 0.6558 time to fit residues: 59.3545 Evaluate side-chains 79 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 245 HIS Chi-restraints excluded: chain F residue 293 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 0.0870 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 0.0870 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.079535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.053190 restraints weight = 16639.319| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.81 r_work: 0.2778 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6170 Z= 0.107 Angle : 0.611 11.029 8397 Z= 0.301 Chirality : 0.043 0.230 943 Planarity : 0.004 0.038 1066 Dihedral : 7.945 179.761 962 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.30 % Rotamer: Outliers : 4.12 % Allowed : 17.07 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.31), residues: 744 helix: 1.85 (1.18), residues: 25 sheet: 1.17 (0.31), residues: 305 loop : -0.93 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 114 TYR 0.012 0.001 TYR B 94 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 6158) covalent geometry : angle 0.57926 / 0.29 ( 8367) SS BOND : bond 0.00265 / 0.14 ( 6) SS BOND : angle 0.63918 / 0.36 ( 12) hydrogen bonds : bond 0.02739 / 1.87 ( 199) hydrogen bonds : angle 5.20899 / 3.52 ( 534) link_BETA1-4 : bond 0.00317 / 0.17 ( 1) link_BETA1-4 : angle 1.36246 / 0.69 ( 3) link_NAG-ASN : bond 0.01115 / 0.54 ( 5) link_NAG-ASN : angle 4.55987 / 2.36 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8611 (m-30) REVERT: A 81 GLU cc_start: 0.8789 (pm20) cc_final: 0.8389 (pm20) REVERT: A 107 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8670 (ttmm) REVERT: A 108 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7404 (ppp80) REVERT: A 142 ARG cc_start: 0.8877 (ttt-90) cc_final: 0.8415 (ttp80) REVERT: A 165 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8474 (pm20) REVERT: A 192 TYR cc_start: 0.8163 (m-80) cc_final: 0.7438 (m-80) REVERT: A 210 ASN cc_start: 0.8856 (m-40) cc_final: 0.8504 (p0) REVERT: A 211 ARG cc_start: 0.9048 (mtp-110) cc_final: 0.8603 (mpp80) REVERT: B 72 ASP cc_start: 0.8371 (t0) cc_final: 0.8033 (t0) REVERT: B 115 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8225 (p) REVERT: E 64 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8580 (mmmm) REVERT: F 218 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8331 (pm20) outliers start: 27 outliers final: 18 residues processed: 92 average time/residue: 0.6703 time to fit residues: 64.1051 Evaluate side-chains 81 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 293 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.0060 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN E 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.079524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.053431 restraints weight = 16467.665| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.78 r_work: 0.2770 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6170 Z= 0.117 Angle : 0.624 10.986 8397 Z= 0.311 Chirality : 0.043 0.226 943 Planarity : 0.004 0.045 1066 Dihedral : 7.789 179.843 960 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.30 % Rotamer: Outliers : 3.81 % Allowed : 17.68 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.31), residues: 744 helix: 1.40 (1.10), residues: 25 sheet: 1.04 (0.31), residues: 311 loop : -0.87 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 114 TYR 0.022 0.001 TYR E 79 PHE 0.009 0.001 PHE E 67 TRP 0.008 0.001 TRP B 47 HIS 0.004 0.000 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6158) covalent geometry : angle 0.59367 / 0.30 ( 8367) SS BOND : bond 0.00316 / 0.16 ( 6) SS BOND : angle 0.86946 / 0.52 ( 12) hydrogen bonds : bond 0.02949 / 2.03 ( 199) hydrogen bonds : angle 5.22366 / 3.53 ( 534) link_BETA1-4 : bond 0.00476 / 0.25 ( 1) link_BETA1-4 : angle 1.35858 / 0.69 ( 3) link_NAG-ASN : bond 0.01078 / 0.52 ( 5) link_NAG-ASN : angle 4.55024 / 2.36 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8608 (m-30) REVERT: A 81 GLU cc_start: 0.8803 (pm20) cc_final: 0.8429 (pm20) REVERT: A 107 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8682 (ttmm) REVERT: A 108 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7403 (ppp80) REVERT: A 124 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8441 (mt0) REVERT: A 142 ARG cc_start: 0.8912 (ttt-90) cc_final: 0.8529 (ttp80) REVERT: A 165 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8470 (pm20) REVERT: A 192 TYR cc_start: 0.8264 (m-80) cc_final: 0.7529 (m-80) REVERT: A 210 ASN cc_start: 0.8901 (m-40) cc_final: 0.8519 (p0) REVERT: A 211 ARG cc_start: 0.9055 (mtp-110) cc_final: 0.8610 (mpp80) REVERT: B 72 ASP cc_start: 0.8424 (t0) cc_final: 0.8087 (t0) REVERT: B 115 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8240 (p) REVERT: F 218 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8352 (pm20) outliers start: 25 outliers final: 18 residues processed: 83 average time/residue: 0.6343 time to fit residues: 54.8333 Evaluate side-chains 78 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 293 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 39 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.079967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.053108 restraints weight = 16530.899| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.85 r_work: 0.2773 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6170 Z= 0.118 Angle : 0.643 10.948 8397 Z= 0.318 Chirality : 0.043 0.226 943 Planarity : 0.004 0.050 1066 Dihedral : 7.802 179.894 960 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.83 % Rotamer: Outliers : 3.96 % Allowed : 17.53 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.31), residues: 744 helix: 1.30 (1.07), residues: 25 sheet: 1.01 (0.31), residues: 311 loop : -0.92 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 114 TYR 0.013 0.001 TYR B 94 PHE 0.009 0.001 PHE F 168 TRP 0.008 0.001 TRP B 47 HIS 0.004 0.000 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 6158) covalent geometry : angle 0.61410 / 0.31 ( 8367) SS BOND : bond 0.00351 / 0.17 ( 6) SS BOND : angle 0.77688 / 0.44 ( 12) hydrogen bonds : bond 0.02887 / 1.97 ( 199) hydrogen bonds : angle 5.20152 / 3.51 ( 534) link_BETA1-4 : bond 0.00351 / 0.18 ( 1) link_BETA1-4 : angle 1.33141 / 0.68 ( 3) link_NAG-ASN : bond 0.01061 / 0.51 ( 5) link_NAG-ASN : angle 4.50913 / 2.32 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8604 (m-30) REVERT: A 81 GLU cc_start: 0.8810 (pm20) cc_final: 0.8435 (pm20) REVERT: A 107 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8675 (ttmm) REVERT: A 108 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7405 (ppp80) REVERT: A 124 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8607 (mm-40) REVERT: A 142 ARG cc_start: 0.8910 (ttt-90) cc_final: 0.8454 (ttp80) REVERT: A 165 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8467 (pm20) REVERT: A 192 TYR cc_start: 0.8260 (m-80) cc_final: 0.7534 (m-80) REVERT: A 210 ASN cc_start: 0.8884 (m-40) cc_final: 0.8501 (p0) REVERT: A 211 ARG cc_start: 0.9066 (mtp-110) cc_final: 0.8612 (mpp80) REVERT: B 72 ASP cc_start: 0.8427 (t0) cc_final: 0.8088 (t0) REVERT: B 115 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8276 (p) REVERT: E 64 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8701 (mmmm) REVERT: F 218 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8365 (pm20) outliers start: 26 outliers final: 17 residues processed: 85 average time/residue: 0.6385 time to fit residues: 56.6010 Evaluate side-chains 82 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 5 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.079907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.053845 restraints weight = 16482.464| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.80 r_work: 0.2770 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6170 Z= 0.119 Angle : 0.638 10.916 8397 Z= 0.317 Chirality : 0.043 0.227 943 Planarity : 0.004 0.050 1066 Dihedral : 7.697 179.877 959 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 3.51 % Allowed : 18.29 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.31), residues: 744 helix: 1.25 (1.07), residues: 25 sheet: 0.99 (0.31), residues: 311 loop : -0.89 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 114 TYR 0.023 0.001 TYR E 79 PHE 0.012 0.001 PHE E 67 TRP 0.008 0.001 TRP B 47 HIS 0.004 0.000 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 6158) covalent geometry : angle 0.60902 / 0.31 ( 8367) SS BOND : bond 0.00333 / 0.17 ( 6) SS BOND : angle 0.91943 / 0.56 ( 12) hydrogen bonds : bond 0.02844 / 1.96 ( 199) hydrogen bonds : angle 5.16214 / 3.50 ( 534) link_BETA1-4 : bond 0.00404 / 0.21 ( 1) link_BETA1-4 : angle 1.32518 / 0.68 ( 3) link_NAG-ASN : bond 0.01051 / 0.51 ( 5) link_NAG-ASN : angle 4.48645 / 2.31 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.06 seconds wall clock time: 43 minutes 18.74 seconds (2598.74 seconds total)