Starting phenix.real_space_refine on Wed Feb 4 00:53:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ecz_47928/02_2026/9ecz_47928_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ecz_47928/02_2026/9ecz_47928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ecz_47928/02_2026/9ecz_47928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ecz_47928/02_2026/9ecz_47928.map" model { file = "/net/cci-nas-00/data/ceres_data/9ecz_47928/02_2026/9ecz_47928_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ecz_47928/02_2026/9ecz_47928_trim.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians S 16 5.16 5 C 2592 2.51 5 N 663 2.21 5 O 801 1.98 5 H 3771 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7843 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 4027 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 14, 'TRANS': 237} Chain breaks: 2 Chain: "H" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1894 Classifications: {'peptide': 127} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "L" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1749 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "B" 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: "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: "E" 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: "D" 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: 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 Time building chain proxies: 1.05, per 1000 atoms: 0.13 Number of scatterers: 7843 At special positions: 0 Unit cell: (79.56, 96.9, 94.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 O 801 8.00 N 663 7.00 C 2592 6.00 H 3771 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " 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 B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " 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-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 149 " " NAG B 1 " - " ASN A 61 " " NAG C 1 " - " ASN A 122 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 234 " Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 108.2 milliseconds 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 906 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 10 sheets defined 2.8% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 196 through 200 removed outlier: 3.849A pdb=" N GLY A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.504A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 4.077A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 71 removed outlier: 7.801A pdb=" N SER A 71 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A 76 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 145 Processing sheet with id=AA5, first strand: chain 'H' and resid 2 through 5 Processing sheet with id=AA6, first strand: chain 'H' and resid 16 through 20 removed outlier: 6.285A pdb=" N VAL H 18 " --> pdb=" O SER H 84 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER H 84 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL H 20 " --> pdb=" O GLU H 82 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLU H 82 " --> pdb=" O VAL H 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.504A pdb=" N GLY H 50 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ILE H 34 " --> pdb=" O PHE H 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.504A pdb=" N GLY H 50 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ILE H 34 " --> pdb=" O PHE H 51 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR H 95 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.711A pdb=" N TYR L 91 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY L 89 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) 91 hydrogen bonds defined for protein. 222 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: 1.34 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3751 1.03 - 1.23: 38 1.23 - 1.43: 1785 1.43 - 1.62: 2347 1.62 - 1.82: 24 Bond restraints: 7945 Sorted by residual: bond pdb=" N ASN A 165 " pdb=" H ASN A 165 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" N ASN A 61 " pdb=" H ASN A 61 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.68e+01 bond pdb=" N ASN A 164 " pdb=" H ASN A 164 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.66e+01 bond pdb=" N ASP A 215 " pdb=" H ASP A 215 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.66e+01 bond pdb=" N CYS A 166 " pdb=" H CYS A 166 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.64e+01 ... (remaining 7940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.37: 14189 7.37 - 14.74: 0 14.74 - 22.11: 0 22.11 - 29.48: 0 29.48 - 36.85: 3 Bond angle restraints: 14192 Sorted by residual: angle pdb=" N THR H 105 " pdb=" CA THR H 105 " pdb=" HA THR H 105 " ideal model delta sigma weight residual 110.00 73.15 36.85 3.00e+00 1.11e-01 1.51e+02 angle pdb=" CB THR H 105 " pdb=" CA THR H 105 " pdb=" HA THR H 105 " ideal model delta sigma weight residual 109.00 75.77 33.23 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C THR H 105 " pdb=" CA THR H 105 " pdb=" HA THR H 105 " ideal model delta sigma weight residual 109.00 77.29 31.71 3.00e+00 1.11e-01 1.12e+02 angle pdb=" CA CYS A 166 " pdb=" C CYS A 166 " pdb=" O CYS A 166 " ideal model delta sigma weight residual 121.78 117.52 4.26 1.28e+00 6.10e-01 1.11e+01 angle pdb=" N THR H 105 " pdb=" CA THR H 105 " pdb=" C THR H 105 " ideal model delta sigma weight residual 109.81 117.12 -7.31 2.21e+00 2.05e-01 1.09e+01 ... (remaining 14187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.92: 3718 23.92 - 47.85: 182 47.85 - 71.77: 55 71.77 - 95.69: 26 95.69 - 119.61: 14 Dihedral angle restraints: 3995 sinusoidal: 2242 harmonic: 1753 Sorted by residual: dihedral pdb=" C1 NAG C 2 " pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C6 NAG C 2 " ideal model delta sinusoidal sigma weight residual 171.16 -69.23 -119.61 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" C1 NAG C 2 " pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C4 NAG C 2 " ideal model delta sinusoidal sigma weight residual -64.11 52.93 -117.04 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" C THR H 105 " pdb=" N THR H 105 " pdb=" CA THR H 105 " pdb=" CB THR H 105 " ideal model delta harmonic sigma weight residual -122.00 -131.78 9.78 0 2.50e+00 1.60e-01 1.53e+01 ... (remaining 3992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 588 0.085 - 0.171: 60 0.171 - 0.256: 7 0.256 - 0.341: 2 0.341 - 0.426: 2 Chirality restraints: 659 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.94e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.47e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.36e+02 ... (remaining 656 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.323 2.00e-02 2.50e+03 2.75e-01 9.46e+02 pdb=" C7 NAG D 2 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.480 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.255 2.00e-02 2.50e+03 2.16e-01 5.81e+02 pdb=" C7 NAG D 1 " 0.059 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.041 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.351 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 164 " 0.064 2.00e-02 2.50e+03 6.21e-02 5.79e+01 pdb=" CG ASN A 164 " -0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN A 164 " -0.063 2.00e-02 2.50e+03 pdb=" ND2 ASN A 164 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 164 " 0.086 2.00e-02 2.50e+03 pdb="HD22 ASN A 164 " -0.087 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 280 2.15 - 2.77: 14615 2.77 - 3.38: 20179 3.38 - 3.99: 25870 3.99 - 4.60: 40190 Nonbonded interactions: 101134 Sorted by model distance: nonbonded pdb=" O VAL L 13 " pdb=" H LYS L 112 " model vdw 1.542 2.450 nonbonded pdb=" OH TYR A 37 " pdb=" HZ1 LYS A 195 " model vdw 1.552 2.450 nonbonded pdb=" OE1 GLN L 95 " pdb=" H GLN L 95 " model vdw 1.552 2.450 nonbonded pdb="HH21 ARG A 34 " pdb=" O PRO A 217 " model vdw 1.606 2.450 nonbonded pdb=" O PRO A 85 " pdb=" HH TYR A 269 " model vdw 1.628 2.450 ... (remaining 101129 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 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 11.830 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: 0.040 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.760 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5322 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 : 0.005 0.060 4191 Z= 0.250 Angle : 0.854 8.691 5722 Z= 0.430 Chirality : 0.056 0.426 659 Planarity : 0.014 0.275 709 Dihedral : 17.835 119.614 1695 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.93 % Allowed : 7.67 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.37), residues: 482 helix: None (None), residues: 0 sheet: -1.57 (0.45), residues: 134 loop : -1.98 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.008 0.001 TYR A 170 PHE 0.008 0.001 PHE A 140 TRP 0.005 0.001 TRP A 258 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 4174) covalent geometry : angle 0.79156 ( 5675) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.66959 ( 8) hydrogen bonds : bond 0.31415 ( 88) hydrogen bonds : angle 10.53505 ( 222) link_BETA1-4 : bond 0.00717 ( 7) link_BETA1-4 : angle 3.98406 ( 21) link_NAG-ASN : bond 0.01815 ( 6) link_NAG-ASN : angle 3.97280 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.7323 (p) cc_final: 0.7060 (p) REVERT: A 109 THR cc_start: 0.6003 (t) cc_final: 0.5768 (t) outliers start: 4 outliers final: 3 residues processed: 144 average time/residue: 0.1282 time to fit residues: 22.4422 Evaluate side-chains 99 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain L residue 101 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.174828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.137419 restraints weight = 21201.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.142069 restraints weight = 10238.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.145206 restraints weight = 6424.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.147251 restraints weight = 4679.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.148627 restraints weight = 3781.188| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 4191 Z= 0.250 Angle : 0.971 9.267 5722 Z= 0.457 Chirality : 0.057 0.448 659 Planarity : 0.006 0.045 709 Dihedral : 13.794 94.814 811 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.37 % Favored : 89.42 % Rotamer: Outliers : 3.26 % Allowed : 12.33 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -1.49 (0.39), residues: 167 loop : -2.15 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 24 TYR 0.027 0.002 TYR A 265 PHE 0.025 0.003 PHE A 186 TRP 0.014 0.002 TRP A 258 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 4174) covalent geometry : angle 0.94238 ( 5675) SS BOND : bond 0.01128 ( 4) SS BOND : angle 0.98013 ( 8) hydrogen bonds : bond 0.05759 ( 88) hydrogen bonds : angle 7.59506 ( 222) link_BETA1-4 : bond 0.01977 ( 7) link_BETA1-4 : angle 3.19119 ( 21) link_NAG-ASN : bond 0.00514 ( 6) link_NAG-ASN : angle 2.67251 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.6310 (t60) cc_final: 0.5927 (t60) REVERT: H 115 MET cc_start: 0.7473 (pmm) cc_final: 0.7115 (pmm) outliers start: 14 outliers final: 10 residues processed: 119 average time/residue: 0.1139 time to fit residues: 16.9346 Evaluate side-chains 104 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 101 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.0570 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.176603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.138621 restraints weight = 21104.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.143400 restraints weight = 10293.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.146649 restraints weight = 6442.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.148734 restraints weight = 4700.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.149970 restraints weight = 3809.171| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4191 Z= 0.142 Angle : 0.720 9.463 5722 Z= 0.343 Chirality : 0.049 0.423 659 Planarity : 0.005 0.044 709 Dihedral : 11.586 86.317 811 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.47 % Favored : 92.32 % Rotamer: Outliers : 3.26 % Allowed : 15.12 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.37), residues: 482 helix: None (None), residues: 0 sheet: -1.42 (0.39), residues: 174 loop : -1.91 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.017 0.002 TYR A 170 PHE 0.014 0.001 PHE L 99 TRP 0.014 0.001 TRP A 258 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4174) covalent geometry : angle 0.68367 ( 5675) SS BOND : bond 0.00366 ( 4) SS BOND : angle 1.11076 ( 8) hydrogen bonds : bond 0.05014 ( 88) hydrogen bonds : angle 7.17780 ( 222) link_BETA1-4 : bond 0.01092 ( 7) link_BETA1-4 : angle 3.08564 ( 21) link_NAG-ASN : bond 0.00478 ( 6) link_NAG-ASN : angle 2.36931 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ASN cc_start: 0.7102 (m-40) cc_final: 0.6900 (m110) REVERT: H 39 GLN cc_start: 0.7623 (tt0) cc_final: 0.7391 (tm-30) REVERT: H 52 ASP cc_start: 0.8283 (t0) cc_final: 0.8043 (t0) REVERT: H 115 MET cc_start: 0.7693 (pmm) cc_final: 0.7264 (pmm) outliers start: 14 outliers final: 8 residues processed: 101 average time/residue: 0.0988 time to fit residues: 12.7831 Evaluate side-chains 98 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain H residue 116 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.174248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.135666 restraints weight = 22011.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.140324 restraints weight = 10958.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.143476 restraints weight = 6952.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.145527 restraints weight = 5125.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.146810 restraints weight = 4175.004| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 4191 Z= 0.227 Angle : 0.821 11.650 5722 Z= 0.401 Chirality : 0.050 0.415 659 Planarity : 0.005 0.043 709 Dihedral : 9.478 59.950 809 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.24 % Favored : 87.55 % Rotamer: Outliers : 2.79 % Allowed : 16.51 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.55 (0.37), residues: 482 helix: None (None), residues: 0 sheet: -1.02 (0.42), residues: 158 loop : -2.17 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.013 0.002 TYR H 95 PHE 0.016 0.002 PHE A 86 TRP 0.013 0.002 TRP A 258 HIS 0.006 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 4174) covalent geometry : angle 0.77563 ( 5675) SS BOND : bond 0.00446 ( 4) SS BOND : angle 1.53174 ( 8) hydrogen bonds : bond 0.06483 ( 88) hydrogen bonds : angle 7.01582 ( 222) link_BETA1-4 : bond 0.01190 ( 7) link_BETA1-4 : angle 3.27242 ( 21) link_NAG-ASN : bond 0.00818 ( 6) link_NAG-ASN : angle 3.33892 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8526 (t) cc_final: 0.8269 (m) REVERT: A 170 TYR cc_start: 0.8132 (t80) cc_final: 0.7768 (t80) REVERT: H 52 ASP cc_start: 0.8379 (t0) cc_final: 0.8072 (t0) outliers start: 12 outliers final: 11 residues processed: 98 average time/residue: 0.1032 time to fit residues: 12.7700 Evaluate side-chains 92 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 6 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 0.0270 chunk 39 optimal weight: 0.9980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.176211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.137043 restraints weight = 21675.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.141656 restraints weight = 10684.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.144955 restraints weight = 6829.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.147043 restraints weight = 5048.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.148239 restraints weight = 4125.560| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.6958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 4191 Z= 0.151 Angle : 0.722 12.361 5722 Z= 0.352 Chirality : 0.049 0.422 659 Planarity : 0.004 0.039 709 Dihedral : 8.149 58.666 809 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.88 % Favored : 91.91 % Rotamer: Outliers : 3.26 % Allowed : 16.98 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.37), residues: 482 helix: None (None), residues: 0 sheet: -1.17 (0.41), residues: 160 loop : -1.92 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.011 0.001 TYR A 204 PHE 0.014 0.002 PHE A 140 TRP 0.016 0.002 TRP A 258 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4174) covalent geometry : angle 0.67477 ( 5675) SS BOND : bond 0.00561 ( 4) SS BOND : angle 3.96137 ( 8) hydrogen bonds : bond 0.04416 ( 88) hydrogen bonds : angle 6.73671 ( 222) link_BETA1-4 : bond 0.01030 ( 7) link_BETA1-4 : angle 2.87541 ( 21) link_NAG-ASN : bond 0.00390 ( 6) link_NAG-ASN : angle 2.38453 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8589 (t) cc_final: 0.8348 (m) REVERT: A 170 TYR cc_start: 0.8154 (t80) cc_final: 0.7839 (t80) REVERT: A 188 ASN cc_start: 0.4526 (t0) cc_final: 0.4279 (t0) REVERT: A 189 LEU cc_start: 0.7773 (tp) cc_final: 0.7541 (tp) REVERT: H 52 ASP cc_start: 0.8315 (t0) cc_final: 0.7990 (t0) REVERT: H 115 MET cc_start: 0.8120 (pmm) cc_final: 0.7161 (pmm) REVERT: H 116 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8195 (m-30) outliers start: 14 outliers final: 12 residues processed: 91 average time/residue: 0.1010 time to fit residues: 11.9443 Evaluate side-chains 90 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.173338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.133572 restraints weight = 21827.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.137963 restraints weight = 11310.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.140987 restraints weight = 7410.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.142927 restraints weight = 5602.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.143764 restraints weight = 4665.124| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.7971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 4191 Z= 0.217 Angle : 0.795 10.198 5722 Z= 0.391 Chirality : 0.050 0.414 659 Planarity : 0.005 0.056 709 Dihedral : 7.875 55.063 809 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.49 % Favored : 86.51 % Rotamer: Outliers : 3.49 % Allowed : 17.67 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -1.48 (0.39), residues: 173 loop : -2.12 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 78 TYR 0.011 0.002 TYR H 111 PHE 0.015 0.002 PHE A 65 TRP 0.014 0.002 TRP A 258 HIS 0.006 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 4174) covalent geometry : angle 0.74672 ( 5675) SS BOND : bond 0.00442 ( 4) SS BOND : angle 2.74506 ( 8) hydrogen bonds : bond 0.05196 ( 88) hydrogen bonds : angle 6.53270 ( 222) link_BETA1-4 : bond 0.01088 ( 7) link_BETA1-4 : angle 3.02842 ( 21) link_NAG-ASN : bond 0.00675 ( 6) link_NAG-ASN : angle 3.28880 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: H 52 ASP cc_start: 0.8358 (t0) cc_final: 0.7983 (t0) REVERT: H 123 THR cc_start: 0.9020 (m) cc_final: 0.8768 (p) outliers start: 15 outliers final: 13 residues processed: 89 average time/residue: 0.0949 time to fit residues: 10.9322 Evaluate side-chains 92 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** 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 = 0.4302 r_free = 0.4302 target = 0.171836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.131968 restraints weight = 22180.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.136368 restraints weight = 11450.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.139396 restraints weight = 7457.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.141351 restraints weight = 5609.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.142749 restraints weight = 4662.226| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.8470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 4191 Z= 0.186 Angle : 0.746 10.444 5722 Z= 0.366 Chirality : 0.048 0.417 659 Planarity : 0.005 0.040 709 Dihedral : 7.607 54.446 809 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.96 % Favored : 89.83 % Rotamer: Outliers : 3.49 % Allowed : 20.00 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -1.34 (0.39), residues: 172 loop : -2.07 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 50 TYR 0.011 0.002 TYR H 111 PHE 0.016 0.002 PHE L 99 TRP 0.018 0.002 TRP A 258 HIS 0.007 0.002 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 4174) covalent geometry : angle 0.69454 ( 5675) SS BOND : bond 0.00482 ( 4) SS BOND : angle 3.37220 ( 8) hydrogen bonds : bond 0.04526 ( 88) hydrogen bonds : angle 6.44196 ( 222) link_BETA1-4 : bond 0.01041 ( 7) link_BETA1-4 : angle 3.09440 ( 21) link_NAG-ASN : bond 0.00404 ( 6) link_NAG-ASN : angle 2.91804 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: A 238 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7211 (p90) REVERT: H 52 ASP cc_start: 0.8336 (t0) cc_final: 0.7975 (t0) REVERT: H 123 THR cc_start: 0.9068 (m) cc_final: 0.8827 (p) outliers start: 15 outliers final: 11 residues processed: 81 average time/residue: 0.0987 time to fit residues: 10.4980 Evaluate side-chains 88 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 116 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** 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 = 0.4256 r_free = 0.4256 target = 0.167546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.127596 restraints weight = 22366.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.131627 restraints weight = 11750.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.134664 restraints weight = 7754.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136544 restraints weight = 5852.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.137844 restraints weight = 4874.613| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.9630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 4191 Z= 0.269 Angle : 0.874 11.770 5722 Z= 0.426 Chirality : 0.051 0.412 659 Planarity : 0.005 0.043 709 Dihedral : 8.261 54.455 809 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.41 % Allowed : 16.18 % Favored : 83.40 % Rotamer: Outliers : 4.19 % Allowed : 20.23 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -1.33 (0.40), residues: 167 loop : -2.60 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 50 TYR 0.016 0.002 TYR A 266 PHE 0.020 0.003 PHE A 106 TRP 0.030 0.003 TRP H 36 HIS 0.008 0.002 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 4174) covalent geometry : angle 0.81228 ( 5675) SS BOND : bond 0.00611 ( 4) SS BOND : angle 3.02775 ( 8) hydrogen bonds : bond 0.05285 ( 88) hydrogen bonds : angle 6.78206 ( 222) link_BETA1-4 : bond 0.01185 ( 7) link_BETA1-4 : angle 3.54400 ( 21) link_NAG-ASN : bond 0.00798 ( 6) link_NAG-ASN : angle 4.04451 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: A 238 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7336 (p90) REVERT: H 3 ARG cc_start: 0.8508 (mmm160) cc_final: 0.8234 (mmm-85) REVERT: H 123 THR cc_start: 0.9122 (m) cc_final: 0.8874 (p) outliers start: 18 outliers final: 10 residues processed: 89 average time/residue: 0.1036 time to fit residues: 11.9768 Evaluate side-chains 88 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 51 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 22 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 11 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 120 GLN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.170054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.131151 restraints weight = 21369.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.135476 restraints weight = 11063.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.138290 restraints weight = 7251.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.140367 restraints weight = 5472.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.141710 restraints weight = 4495.664| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.9871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4191 Z= 0.145 Angle : 0.760 10.297 5722 Z= 0.367 Chirality : 0.050 0.417 659 Planarity : 0.004 0.040 709 Dihedral : 7.653 53.327 809 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.17 % Favored : 89.63 % Rotamer: Outliers : 2.79 % Allowed : 21.63 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -1.15 (0.40), residues: 166 loop : -2.23 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 50 TYR 0.014 0.002 TYR H 111 PHE 0.025 0.002 PHE A 140 TRP 0.020 0.002 TRP A 258 HIS 0.005 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 4174) covalent geometry : angle 0.71065 ( 5675) SS BOND : bond 0.00470 ( 4) SS BOND : angle 2.91160 ( 8) hydrogen bonds : bond 0.04333 ( 88) hydrogen bonds : angle 6.52161 ( 222) link_BETA1-4 : bond 0.00999 ( 7) link_BETA1-4 : angle 3.26261 ( 21) link_NAG-ASN : bond 0.00326 ( 6) link_NAG-ASN : angle 2.83659 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: A 238 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7456 (p90) REVERT: H 3 ARG cc_start: 0.8490 (mmm160) cc_final: 0.8100 (mmm-85) REVERT: H 52 ASP cc_start: 0.8382 (t0) cc_final: 0.7985 (t0) REVERT: H 123 THR cc_start: 0.9063 (m) cc_final: 0.8792 (p) outliers start: 12 outliers final: 8 residues processed: 87 average time/residue: 0.1113 time to fit residues: 12.4418 Evaluate side-chains 86 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 40 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.168159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.129037 restraints weight = 21686.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.133072 restraints weight = 11328.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136005 restraints weight = 7501.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.137921 restraints weight = 5669.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.139148 restraints weight = 4702.937| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 1.0243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 4191 Z= 0.210 Angle : 0.803 9.505 5722 Z= 0.386 Chirality : 0.049 0.415 659 Planarity : 0.005 0.038 709 Dihedral : 7.682 54.400 809 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.49 % Favored : 86.31 % Rotamer: Outliers : 2.33 % Allowed : 22.79 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -1.16 (0.43), residues: 156 loop : -2.47 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 190 TYR 0.014 0.002 TYR A 266 PHE 0.017 0.002 PHE A 140 TRP 0.013 0.002 TRP A 258 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 4174) covalent geometry : angle 0.75015 ( 5675) SS BOND : bond 0.00478 ( 4) SS BOND : angle 2.98947 ( 8) hydrogen bonds : bond 0.04778 ( 88) hydrogen bonds : angle 6.47445 ( 222) link_BETA1-4 : bond 0.01136 ( 7) link_BETA1-4 : angle 3.32381 ( 21) link_NAG-ASN : bond 0.00559 ( 6) link_NAG-ASN : angle 3.24554 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7205 (m-80) cc_final: 0.6801 (m-80) REVERT: A 80 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8131 (m-30) REVERT: A 238 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7477 (p90) REVERT: H 3 ARG cc_start: 0.8553 (mmm160) cc_final: 0.8149 (mmm-85) REVERT: H 52 ASP cc_start: 0.8467 (t0) cc_final: 0.8029 (t0) REVERT: H 123 THR cc_start: 0.9095 (m) cc_final: 0.8821 (p) outliers start: 10 outliers final: 8 residues processed: 84 average time/residue: 0.1062 time to fit residues: 11.4652 Evaluate side-chains 88 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 40 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 21 optimal weight: 0.0470 chunk 1 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.171146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.131761 restraints weight = 21245.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.136106 restraints weight = 10889.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.139167 restraints weight = 7094.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.141238 restraints weight = 5322.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.142490 restraints weight = 4363.054| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 1.0320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4191 Z= 0.132 Angle : 0.731 10.177 5722 Z= 0.351 Chirality : 0.049 0.412 659 Planarity : 0.004 0.041 709 Dihedral : 7.281 53.701 809 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.71 % Favored : 91.08 % Rotamer: Outliers : 2.79 % Allowed : 22.56 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.37), residues: 482 helix: None (None), residues: 0 sheet: -0.84 (0.42), residues: 163 loop : -2.18 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.012 0.001 TYR H 111 PHE 0.016 0.002 PHE A 92 TRP 0.013 0.001 TRP A 258 HIS 0.004 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4174) covalent geometry : angle 0.68956 ( 5675) SS BOND : bond 0.00431 ( 4) SS BOND : angle 2.74010 ( 8) hydrogen bonds : bond 0.04099 ( 88) hydrogen bonds : angle 6.29182 ( 222) link_BETA1-4 : bond 0.01038 ( 7) link_BETA1-4 : angle 3.11836 ( 21) link_NAG-ASN : bond 0.00256 ( 6) link_NAG-ASN : angle 2.32638 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1920.56 seconds wall clock time: 33 minutes 18.90 seconds (1998.90 seconds total)