Starting phenix.real_space_refine on Tue Aug 4 18:40:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w0e_65503/08_2026/9w0e_65503.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w0e_65503/08_2026/9w0e_65503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w0e_65503/08_2026/9w0e_65503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w0e_65503/08_2026/9w0e_65503.map" model { file = "/net/cci-nas-00/data/ceres_data/9w0e_65503/08_2026/9w0e_65503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w0e_65503/08_2026/9w0e_65503.cif" } resolution = 2.93 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= 0.004 sd= 0.080 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 3794 2.51 5 N 1009 2.21 5 O 1133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5977 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1933 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 230} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1848 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 217} Chain: "C" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1901 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 119 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "E" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.33, per 1000 atoms: 0.22 Number of scatterers: 5977 At special positions: 0 Unit cell: (100.225, 100.225, 80.18, 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 41 16.00 O 1133 8.00 N 1009 7.00 C 3794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... BETA2-6 " GAL G 1 " - " SIA G 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 367.9 milliseconds 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 11 sheets defined 13.0% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.821A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.648A pdb=" N TRP A 163 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 164 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 165 " --> pdb=" O HIS A 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'C' and resid 43 through 48 removed outlier: 3.507A pdb=" N ILE C 47 " --> pdb=" O MET C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.567A pdb=" N GLU C 65 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'E' and resid 201 through 205 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 76 removed outlier: 6.564A pdb=" N VAL A 239 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 71 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 237 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER A 73 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 235 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU A 75 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE A 233 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 184 removed outlier: 4.843A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA A 248 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 removed outlier: 4.090A pdb=" N ALA A 169 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'B' and resid 69 through 71 removed outlier: 4.547A pdb=" N VAL B 226 " --> pdb=" O TRP B 71 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.606A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 51 through 53 removed outlier: 4.656A pdb=" N GLY C 214 " --> pdb=" O MET C 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 51 through 53 removed outlier: 4.656A pdb=" N GLY C 214 " --> pdb=" O MET C 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.807A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C 199 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR C 126 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.363A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 372 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: 0.94 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1679 1.33 - 1.45: 1068 1.45 - 1.57: 3317 1.57 - 1.69: 1 1.69 - 1.81: 68 Bond restraints: 6133 Sorted by residual: bond pdb=" CA HIS C 240 " pdb=" C HIS C 240 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.33e-02 5.65e+03 6.13e+00 bond pdb=" CA ALA C 242 " pdb=" C ALA C 242 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.35e-02 5.49e+03 4.66e+00 bond pdb=" C HIS C 240 " pdb=" O HIS C 240 " ideal model delta sigma weight residual 1.235 1.212 0.022 1.20e-02 6.94e+03 3.49e+00 bond pdb=" N ALA C 242 " pdb=" CA ALA C 242 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.28e-02 6.10e+03 3.47e+00 bond pdb=" CA LEU C 239 " pdb=" C LEU C 239 " ideal model delta sigma weight residual 1.527 1.503 0.024 1.34e-02 5.57e+03 3.15e+00 ... (remaining 6128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 8149 1.62 - 3.24: 181 3.24 - 4.87: 20 4.87 - 6.49: 3 6.49 - 8.11: 3 Bond angle restraints: 8356 Sorted by residual: angle pdb=" N SER C 236 " pdb=" CA SER C 236 " pdb=" C SER C 236 " ideal model delta sigma weight residual 113.12 105.01 8.11 1.25e+00 6.40e-01 4.21e+01 angle pdb=" CA GLN C 160 " pdb=" CB GLN C 160 " pdb=" CG GLN C 160 " ideal model delta sigma weight residual 114.10 121.63 -7.53 2.00e+00 2.50e-01 1.42e+01 angle pdb=" N GLY C 241 " pdb=" CA GLY C 241 " pdb=" C GLY C 241 " ideal model delta sigma weight residual 115.27 110.50 4.77 1.41e+00 5.03e-01 1.15e+01 angle pdb=" CB GLN C 160 " pdb=" CG GLN C 160 " pdb=" CD GLN C 160 " ideal model delta sigma weight residual 112.60 117.92 -5.32 1.70e+00 3.46e-01 9.79e+00 angle pdb=" C ILE A 294 " pdb=" N VAL A 295 " pdb=" CA VAL A 295 " ideal model delta sigma weight residual 123.12 119.37 3.75 1.30e+00 5.92e-01 8.31e+00 ... (remaining 8351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 3364 21.92 - 43.84: 292 43.84 - 65.75: 47 65.75 - 87.67: 18 87.67 - 109.59: 8 Dihedral angle restraints: 3729 sinusoidal: 1555 harmonic: 2174 Sorted by residual: dihedral pdb=" C2 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" C5 MAN F 4 " ideal model delta sinusoidal sigma weight residual 54.75 -54.84 109.59 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C2 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" O4 MAN F 4 " ideal model delta sinusoidal sigma weight residual 176.13 67.18 108.95 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C5 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" O3 MAN F 4 " ideal model delta sinusoidal sigma weight residual -174.53 -66.13 -108.40 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 3726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 694 0.041 - 0.082: 182 0.082 - 0.123: 66 0.123 - 0.164: 10 0.164 - 0.205: 1 Chirality restraints: 953 Sorted by residual: chirality pdb=" C2 SIA G 2 " pdb=" O6 GAL G 1 " pdb=" C1 SIA G 2 " pdb=" O6 SIA G 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.47 -0.03 2.00e-02 2.50e+03 2.25e+00 chirality pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" O3 BMA F 3 " both_signs ideal model delta sigma weight residual False 2.41 2.20 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE C 170 " pdb=" CA ILE C 170 " pdb=" CG1 ILE C 170 " pdb=" CG2 ILE C 170 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 950 not shown) Planarity restraints: 1065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 26 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C GLN B 26 " -0.025 2.00e-02 2.50e+03 pdb=" O GLN B 26 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU B 27 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 200 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO B 201 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 89 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ILE B 89 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE B 89 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY B 90 " 0.008 2.00e-02 2.50e+03 ... (remaining 1062 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.98: 2977 2.98 - 3.46: 5558 3.46 - 3.94: 9875 3.94 - 4.42: 11746 4.42 - 4.90: 19191 Nonbonded interactions: 49347 Sorted by model distance: nonbonded pdb=" N GLN C 160 " pdb=" OE1 GLN C 160 " model vdw 2.495 3.120 nonbonded pdb=" C6 GAL G 1 " pdb=" O6 SIA G 2 " model vdw 2.499 2.752 nonbonded pdb=" O VAL A 295 " pdb=" C THR A 296 " model vdw 2.512 3.270 nonbonded pdb=" O5 NAG F 1 " pdb=" O6 NAG F 1 " model vdw 2.536 2.432 nonbonded pdb=" N ASN C 237 " pdb=" O ASN C 237 " model vdw 2.554 2.496 ... (remaining 49342 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: 0.590 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.980 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.004 0.037 6139 Z= 0.183 Angle : 0.589 8.112 8374 Z= 0.319 Chirality : 0.043 0.205 953 Planarity : 0.004 0.041 1065 Dihedral : 17.391 109.591 2327 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.93 % Allowed : 23.77 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.86 (0.29), residues: 741 helix: -2.44 (0.64), residues: 54 sheet: 0.16 (0.37), residues: 190 loop : -0.64 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 41 TYR 0.011 0.001 TYR D 37 PHE 0.011 0.001 PHE A 62 TRP 0.009 0.001 TRP C 155 HIS 0.004 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 ( 6133) covalent geometry : angle 0.58242 / 0.32 ( 8356) hydrogen bonds : bond 0.18216 / 12.47 ( 149) hydrogen bonds : angle 8.86602 / 6.18 ( 372) glycosidic custom : bond 0.00020 / 0.01 ( 1) glycosidic custom : angle 0.54677 / 0.29 ( 3) link_ALPHA1-3 : bond 0.00591 / 0.31 ( 1) link_ALPHA1-3 : angle 3.30089 / 1.72 ( 3) link_ALPHA1-6 : bond 0.00728 / 0.38 ( 1) link_ALPHA1-6 : angle 1.27041 / 0.71 ( 3) link_BETA1-4 : bond 0.00143 / 0.07 ( 2) link_BETA1-4 : angle 2.34445 / 1.74 ( 6) link_BETA1-6 : bond 0.00656 / 0.35 ( 1) link_BETA1-6 : angle 1.15800 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.146 Fit side-chains REVERT: A 55 SER cc_start: 0.8870 (m) cc_final: 0.8517 (p) REVERT: A 136 MET cc_start: 0.5652 (ttt) cc_final: 0.3639 (mtp) REVERT: A 164 GLN cc_start: 0.7970 (mp10) cc_final: 0.7013 (tt0) REVERT: A 187 MET cc_start: 0.8277 (ptp) cc_final: 0.7749 (ppp) REVERT: A 268 LYS cc_start: 0.8395 (tttp) cc_final: 0.8020 (ttmt) REVERT: B 147 MET cc_start: 0.9077 (mmt) cc_final: 0.8724 (mmm) REVERT: C 98 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8370 (mt) REVERT: C 124 MET cc_start: 0.8754 (mmm) cc_final: 0.8363 (mmt) REVERT: C 142 THR cc_start: 0.8950 (p) cc_final: 0.8734 (m) REVERT: C 143 THR cc_start: 0.7897 (p) cc_final: 0.7402 (t) REVERT: C 212 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8738 (mt) REVERT: E 205 ARG cc_start: 0.8383 (ppt170) cc_final: 0.8158 (ppt170) outliers start: 19 outliers final: 15 residues processed: 104 average time/residue: 0.4459 time to fit residues: 48.7839 Evaluate side-chains 108 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN B 55 GLN B 88 ASN B 131 GLN B 206 GLN C 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.096559 restraints weight = 8113.628| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.10 r_work: 0.2948 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6139 Z= 0.161 Angle : 0.541 8.208 8374 Z= 0.270 Chirality : 0.043 0.170 953 Planarity : 0.004 0.029 1065 Dihedral : 9.357 74.236 992 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.48 % Allowed : 20.52 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.81 (0.29), residues: 741 helix: -2.41 (0.64), residues: 54 sheet: 0.22 (0.39), residues: 179 loop : -0.60 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 41 TYR 0.010 0.001 TYR A 193 PHE 0.012 0.001 PHE A 62 TRP 0.007 0.001 TRP C 155 HIS 0.002 0.000 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 6133) covalent geometry : angle 0.53458 / 0.27 ( 8356) hydrogen bonds : bond 0.03787 / 2.75 ( 149) hydrogen bonds : angle 6.54760 / 4.51 ( 372) glycosidic custom : bond 0.00097 / 0.05 ( 1) glycosidic custom : angle 0.85135 / 0.46 ( 3) link_ALPHA1-3 : bond 0.00773 / 0.41 ( 1) link_ALPHA1-3 : angle 2.34233 / 1.23 ( 3) link_ALPHA1-6 : bond 0.00753 / 0.40 ( 1) link_ALPHA1-6 : angle 1.29132 / 0.73 ( 3) link_BETA1-4 : bond 0.00145 / 0.07 ( 2) link_BETA1-4 : angle 2.36939 / 1.81 ( 6) link_BETA1-6 : bond 0.00696 / 0.37 ( 1) link_BETA1-6 : angle 1.10558 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.137 Fit side-chains REVERT: A 55 SER cc_start: 0.8969 (m) cc_final: 0.8600 (p) REVERT: A 136 MET cc_start: 0.5718 (ttt) cc_final: 0.3607 (mtp) REVERT: A 164 GLN cc_start: 0.8058 (mp10) cc_final: 0.7095 (tt0) REVERT: A 182 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8355 (ptm) REVERT: A 187 MET cc_start: 0.8300 (ptp) cc_final: 0.7701 (ppp) REVERT: A 268 LYS cc_start: 0.8436 (tttp) cc_final: 0.8056 (ttmt) REVERT: A 271 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7682 (t70) REVERT: B 97 GLN cc_start: 0.8266 (mm110) cc_final: 0.7827 (mm-40) REVERT: B 147 MET cc_start: 0.9033 (mmt) cc_final: 0.8746 (mmm) REVERT: C 98 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8152 (mm) REVERT: C 124 MET cc_start: 0.8758 (mmm) cc_final: 0.8455 (mmt) REVERT: C 142 THR cc_start: 0.8973 (p) cc_final: 0.8771 (m) REVERT: C 143 THR cc_start: 0.7773 (p) cc_final: 0.7070 (t) REVERT: E 205 ARG cc_start: 0.8309 (ppt170) cc_final: 0.8049 (ppt170) outliers start: 29 outliers final: 13 residues processed: 111 average time/residue: 0.4241 time to fit residues: 49.5655 Evaluate side-chains 106 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 79 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 = 0.3397 r_free = 0.3397 target = 0.122362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.096871 restraints weight = 8090.330| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.11 r_work: 0.2897 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6139 Z= 0.183 Angle : 0.534 6.836 8374 Z= 0.268 Chirality : 0.043 0.160 953 Planarity : 0.004 0.038 1065 Dihedral : 7.386 74.400 982 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.25 % Allowed : 19.75 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.72 (0.29), residues: 741 helix: -2.31 (0.64), residues: 54 sheet: 0.28 (0.39), residues: 176 loop : -0.53 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 41 TYR 0.018 0.001 TYR D 37 PHE 0.012 0.001 PHE A 62 TRP 0.008 0.001 TRP C 155 HIS 0.002 0.000 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 6133) covalent geometry : angle 0.52515 / 0.27 ( 8356) hydrogen bonds : bond 0.03377 / 2.48 ( 149) hydrogen bonds : angle 6.06500 / 4.17 ( 372) glycosidic custom : bond 0.00121 / 0.06 ( 1) glycosidic custom : angle 0.80890 / 0.43 ( 3) link_ALPHA1-3 : bond 0.00152 / 0.08 ( 1) link_ALPHA1-3 : angle 3.30185 / 1.74 ( 3) link_ALPHA1-6 : bond 0.00718 / 0.38 ( 1) link_ALPHA1-6 : angle 1.26333 / 0.71 ( 3) link_BETA1-4 : bond 0.00083 / 0.04 ( 2) link_BETA1-4 : angle 2.54507 / 1.84 ( 6) link_BETA1-6 : bond 0.00591 / 0.31 ( 1) link_BETA1-6 : angle 1.01127 / 0.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.242 Fit side-chains REVERT: A 55 SER cc_start: 0.8979 (m) cc_final: 0.8598 (p) REVERT: A 136 MET cc_start: 0.5722 (ttt) cc_final: 0.3571 (mtp) REVERT: A 164 GLN cc_start: 0.8071 (mp10) cc_final: 0.7084 (tt0) REVERT: A 187 MET cc_start: 0.8272 (ptp) cc_final: 0.7736 (ppp) REVERT: A 268 LYS cc_start: 0.8452 (tttp) cc_final: 0.8062 (ttmt) REVERT: A 271 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7658 (t70) REVERT: B 41 TYR cc_start: 0.8269 (m-80) cc_final: 0.8063 (m-80) REVERT: C 48 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8816 (mt0) REVERT: C 124 MET cc_start: 0.8760 (mmm) cc_final: 0.8442 (mmt) REVERT: C 143 THR cc_start: 0.7787 (p) cc_final: 0.7378 (t) REVERT: C 212 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8725 (mp) REVERT: E 205 ARG cc_start: 0.8268 (ppt170) cc_final: 0.7683 (ppt170) outliers start: 34 outliers final: 19 residues processed: 111 average time/residue: 0.3907 time to fit residues: 45.8304 Evaluate side-chains 112 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 48 GLN Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 79 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 = 0.3392 r_free = 0.3392 target = 0.122047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.096617 restraints weight = 8068.502| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.09 r_work: 0.2922 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6139 Z= 0.155 Angle : 0.512 6.773 8374 Z= 0.256 Chirality : 0.042 0.174 953 Planarity : 0.004 0.029 1065 Dihedral : 7.308 74.083 982 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.94 % Allowed : 19.91 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.62 (0.30), residues: 741 helix: -2.19 (0.66), residues: 54 sheet: 0.30 (0.39), residues: 179 loop : -0.45 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 41 TYR 0.015 0.001 TYR D 37 PHE 0.010 0.001 PHE A 62 TRP 0.008 0.001 TRP C 155 HIS 0.002 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 6133) covalent geometry : angle 0.50328 / 0.25 ( 8356) hydrogen bonds : bond 0.02989 / 2.22 ( 149) hydrogen bonds : angle 5.77832 / 3.96 ( 372) glycosidic custom : bond 0.00020 / 0.01 ( 1) glycosidic custom : angle 0.77990 / 0.42 ( 3) link_ALPHA1-3 : bond 0.00221 / 0.12 ( 1) link_ALPHA1-3 : angle 3.48514 / 1.83 ( 3) link_ALPHA1-6 : bond 0.00724 / 0.38 ( 1) link_ALPHA1-6 : angle 1.26674 / 0.71 ( 3) link_BETA1-4 : bond 0.00063 / 0.03 ( 2) link_BETA1-4 : angle 2.39936 / 1.75 ( 6) link_BETA1-6 : bond 0.00550 / 0.29 ( 1) link_BETA1-6 : angle 1.07094 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.226 Fit side-chains REVERT: A 55 SER cc_start: 0.8968 (m) cc_final: 0.8594 (p) REVERT: A 136 MET cc_start: 0.5671 (ttt) cc_final: 0.3552 (mtp) REVERT: A 164 GLN cc_start: 0.8072 (mp10) cc_final: 0.7098 (tt0) REVERT: A 187 MET cc_start: 0.8217 (ptp) cc_final: 0.7712 (ppp) REVERT: A 268 LYS cc_start: 0.8418 (tttp) cc_final: 0.8031 (ttmt) REVERT: A 271 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7678 (t70) REVERT: C 48 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8802 (mt0) REVERT: C 124 MET cc_start: 0.8748 (mmm) cc_final: 0.8453 (mmt) REVERT: C 142 THR cc_start: 0.9142 (p) cc_final: 0.8854 (m) REVERT: C 143 THR cc_start: 0.7793 (p) cc_final: 0.7217 (t) REVERT: C 212 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8695 (mp) REVERT: E 205 ARG cc_start: 0.8188 (ppt170) cc_final: 0.7699 (ppt170) outliers start: 32 outliers final: 18 residues processed: 111 average time/residue: 0.4114 time to fit residues: 48.0207 Evaluate side-chains 112 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 48 GLN Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 79 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 = 0.3401 r_free = 0.3401 target = 0.122665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.097283 restraints weight = 8213.001| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.10 r_work: 0.2914 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6139 Z= 0.177 Angle : 0.523 6.798 8374 Z= 0.261 Chirality : 0.043 0.181 953 Planarity : 0.004 0.030 1065 Dihedral : 7.275 74.036 982 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.86 % Allowed : 19.44 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.29), residues: 741 helix: -2.13 (0.65), residues: 54 sheet: 0.32 (0.39), residues: 179 loop : -0.47 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 41 TYR 0.011 0.001 TYR D 37 PHE 0.011 0.001 PHE A 62 TRP 0.008 0.001 TRP C 155 HIS 0.002 0.000 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 6133) covalent geometry : angle 0.51498 / 0.26 ( 8356) hydrogen bonds : bond 0.02908 / 2.12 ( 149) hydrogen bonds : angle 5.66092 / 3.88 ( 372) glycosidic custom : bond 0.00046 / 0.02 ( 1) glycosidic custom : angle 0.81922 / 0.44 ( 3) link_ALPHA1-3 : bond 0.00288 / 0.15 ( 1) link_ALPHA1-3 : angle 3.32975 / 1.74 ( 3) link_ALPHA1-6 : bond 0.00736 / 0.39 ( 1) link_ALPHA1-6 : angle 1.27390 / 0.71 ( 3) link_BETA1-4 : bond 0.00114 / 0.06 ( 2) link_BETA1-4 : angle 2.33993 / 1.72 ( 6) link_BETA1-6 : bond 0.00547 / 0.29 ( 1) link_BETA1-6 : angle 1.02737 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.225 Fit side-chains REVERT: A 55 SER cc_start: 0.8966 (m) cc_final: 0.8591 (p) REVERT: A 136 MET cc_start: 0.5703 (ttt) cc_final: 0.3599 (mtp) REVERT: A 164 GLN cc_start: 0.8087 (mp10) cc_final: 0.7105 (tt0) REVERT: A 187 MET cc_start: 0.8251 (ptp) cc_final: 0.7749 (ppp) REVERT: A 268 LYS cc_start: 0.8437 (tttp) cc_final: 0.8040 (ttmt) REVERT: A 271 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7700 (t70) REVERT: C 48 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8806 (mt0) REVERT: C 124 MET cc_start: 0.8749 (mmm) cc_final: 0.8465 (mmt) REVERT: C 143 THR cc_start: 0.7777 (p) cc_final: 0.7360 (t) REVERT: C 212 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8684 (mp) outliers start: 38 outliers final: 20 residues processed: 117 average time/residue: 0.4066 time to fit residues: 50.1322 Evaluate side-chains 115 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 38 TRP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 48 GLN Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 0.2980 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 GLN ** C 79 GLN ** 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 = 0.3387 r_free = 0.3387 target = 0.121697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096298 restraints weight = 8078.862| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.10 r_work: 0.2886 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6139 Z= 0.221 Angle : 0.555 7.214 8374 Z= 0.277 Chirality : 0.044 0.188 953 Planarity : 0.004 0.033 1065 Dihedral : 7.139 74.433 981 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.63 % Allowed : 21.14 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.74 (0.29), residues: 741 helix: -2.20 (0.62), residues: 56 sheet: 0.23 (0.39), residues: 178 loop : -0.54 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 41 TYR 0.009 0.001 TYR D 37 PHE 0.012 0.001 PHE A 62 TRP 0.008 0.001 TRP A 163 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 ( 6133) covalent geometry : angle 0.54739 / 0.28 ( 8356) hydrogen bonds : bond 0.02974 / 2.13 ( 149) hydrogen bonds : angle 5.69490 / 3.90 ( 372) glycosidic custom : bond 0.00140 / 0.07 ( 1) glycosidic custom : angle 0.93216 / 0.50 ( 3) link_ALPHA1-3 : bond 0.00245 / 0.13 ( 1) link_ALPHA1-3 : angle 3.34510 / 1.75 ( 3) link_ALPHA1-6 : bond 0.00715 / 0.38 ( 1) link_ALPHA1-6 : angle 1.27649 / 0.72 ( 3) link_BETA1-4 : bond 0.00170 / 0.09 ( 2) link_BETA1-4 : angle 2.39333 / 1.76 ( 6) link_BETA1-6 : bond 0.00550 / 0.29 ( 1) link_BETA1-6 : angle 1.02116 / 0.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.141 Fit side-chains REVERT: A 55 SER cc_start: 0.9032 (m) cc_final: 0.8653 (p) REVERT: A 136 MET cc_start: 0.5728 (ttt) cc_final: 0.3503 (mtp) REVERT: A 164 GLN cc_start: 0.8033 (mp10) cc_final: 0.7199 (pt0) REVERT: A 187 MET cc_start: 0.8286 (ptp) cc_final: 0.7768 (ppp) REVERT: A 268 LYS cc_start: 0.8453 (tttp) cc_final: 0.8049 (ttmt) REVERT: A 271 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7674 (t70) REVERT: B 97 GLN cc_start: 0.8226 (mm110) cc_final: 0.7759 (mm110) REVERT: C 48 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8819 (mt0) REVERT: C 124 MET cc_start: 0.8769 (mmm) cc_final: 0.8516 (mmt) REVERT: C 143 THR cc_start: 0.7760 (p) cc_final: 0.7339 (t) REVERT: C 212 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8706 (mp) REVERT: E 205 ARG cc_start: 0.8009 (ppt170) cc_final: 0.7692 (ppt170) outliers start: 30 outliers final: 20 residues processed: 113 average time/residue: 0.4394 time to fit residues: 52.3233 Evaluate side-chains 115 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 48 GLN Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.098327 restraints weight = 8047.417| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.10 r_work: 0.2930 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6139 Z= 0.132 Angle : 0.509 7.818 8374 Z= 0.253 Chirality : 0.042 0.184 953 Planarity : 0.004 0.030 1065 Dihedral : 6.972 72.795 981 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.48 % Allowed : 21.60 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.59 (0.30), residues: 741 helix: -1.90 (0.67), residues: 54 sheet: 0.26 (0.39), residues: 178 loop : -0.43 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 41 TYR 0.012 0.001 TYR D 37 PHE 0.008 0.001 PHE C 157 TRP 0.008 0.001 TRP C 155 HIS 0.003 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 6133) covalent geometry : angle 0.50076 / 0.25 ( 8356) hydrogen bonds : bond 0.02621 / 1.89 ( 149) hydrogen bonds : angle 5.50285 / 3.76 ( 372) glycosidic custom : bond 0.00086 / 0.05 ( 1) glycosidic custom : angle 0.71837 / 0.38 ( 3) link_ALPHA1-3 : bond 0.00342 / 0.18 ( 1) link_ALPHA1-3 : angle 3.35155 / 1.76 ( 3) link_ALPHA1-6 : bond 0.00772 / 0.41 ( 1) link_ALPHA1-6 : angle 1.25873 / 0.70 ( 3) link_BETA1-4 : bond 0.00149 / 0.07 ( 2) link_BETA1-4 : angle 2.20951 / 1.66 ( 6) link_BETA1-6 : bond 0.00529 / 0.28 ( 1) link_BETA1-6 : angle 1.11497 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.169 Fit side-chains REVERT: A 55 SER cc_start: 0.8950 (m) cc_final: 0.8583 (p) REVERT: A 136 MET cc_start: 0.5685 (ttt) cc_final: 0.3572 (mtp) REVERT: A 164 GLN cc_start: 0.8209 (mp10) cc_final: 0.7217 (tt0) REVERT: A 187 MET cc_start: 0.8203 (ptp) cc_final: 0.7733 (ppp) REVERT: A 268 LYS cc_start: 0.8440 (tttp) cc_final: 0.8056 (ttmt) REVERT: A 271 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7645 (t70) REVERT: B 97 GLN cc_start: 0.8128 (mm110) cc_final: 0.7679 (mm110) REVERT: B 147 MET cc_start: 0.9005 (mmt) cc_final: 0.8770 (mmm) REVERT: B 162 ASP cc_start: 0.9245 (m-30) cc_final: 0.8892 (m-30) REVERT: C 48 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8772 (mt0) REVERT: C 124 MET cc_start: 0.8753 (mmm) cc_final: 0.8398 (mmt) REVERT: C 146 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8341 (p) REVERT: C 212 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8731 (mp) outliers start: 29 outliers final: 17 residues processed: 108 average time/residue: 0.4194 time to fit residues: 47.7283 Evaluate side-chains 109 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 48 GLN Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 41 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 79 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 = 0.3448 r_free = 0.3448 target = 0.126034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101062 restraints weight = 7980.432| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.05 r_work: 0.2976 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6139 Z= 0.111 Angle : 0.498 8.085 8374 Z= 0.247 Chirality : 0.041 0.183 953 Planarity : 0.004 0.030 1065 Dihedral : 6.835 71.500 981 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.24 % Allowed : 22.99 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.57 (0.30), residues: 741 helix: -1.86 (0.66), residues: 55 sheet: 0.25 (0.39), residues: 181 loop : -0.41 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 41 TYR 0.012 0.001 TYR D 37 PHE 0.008 0.001 PHE C 157 TRP 0.009 0.001 TRP C 155 HIS 0.002 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 6133) covalent geometry : angle 0.48987 / 0.25 ( 8356) hydrogen bonds : bond 0.02487 / 1.79 ( 149) hydrogen bonds : angle 5.32963 / 3.64 ( 372) glycosidic custom : bond 0.00155 / 0.08 ( 1) glycosidic custom : angle 0.73865 / 0.39 ( 3) link_ALPHA1-3 : bond 0.00374 / 0.20 ( 1) link_ALPHA1-3 : angle 3.30297 / 1.73 ( 3) link_ALPHA1-6 : bond 0.00788 / 0.41 ( 1) link_ALPHA1-6 : angle 1.27913 / 0.71 ( 3) link_BETA1-4 : bond 0.00129 / 0.06 ( 2) link_BETA1-4 : angle 2.15482 / 1.61 ( 6) link_BETA1-6 : bond 0.00541 / 0.28 ( 1) link_BETA1-6 : angle 1.11537 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.222 Fit side-chains REVERT: A 55 SER cc_start: 0.8923 (m) cc_final: 0.8567 (p) REVERT: A 136 MET cc_start: 0.5638 (ttt) cc_final: 0.3508 (mtp) REVERT: A 164 GLN cc_start: 0.8261 (mp10) cc_final: 0.7177 (tt0) REVERT: A 187 MET cc_start: 0.8160 (ptp) cc_final: 0.7669 (ppp) REVERT: A 268 LYS cc_start: 0.8413 (tttp) cc_final: 0.8030 (ttmt) REVERT: A 271 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7582 (t70) REVERT: B 97 GLN cc_start: 0.8073 (mm110) cc_final: 0.7637 (mm110) REVERT: B 147 MET cc_start: 0.8966 (mmt) cc_final: 0.8720 (mmm) REVERT: C 48 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8744 (mt0) REVERT: C 124 MET cc_start: 0.8736 (mmm) cc_final: 0.8407 (mmt) REVERT: C 212 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8705 (mt) outliers start: 21 outliers final: 16 residues processed: 103 average time/residue: 0.4296 time to fit residues: 46.5944 Evaluate side-chains 107 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 48 GLN Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.094661 restraints weight = 8131.544| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.11 r_work: 0.2833 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6139 Z= 0.210 Angle : 0.554 8.210 8374 Z= 0.276 Chirality : 0.043 0.192 953 Planarity : 0.004 0.032 1065 Dihedral : 6.946 73.401 980 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.24 % Allowed : 23.46 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.67 (0.29), residues: 741 helix: -1.93 (0.65), residues: 56 sheet: 0.18 (0.38), residues: 186 loop : -0.49 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 41 TYR 0.008 0.001 TYR D 37 PHE 0.011 0.001 PHE A 62 TRP 0.007 0.001 TRP C 155 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 ( 6133) covalent geometry : angle 0.54632 / 0.27 ( 8356) hydrogen bonds : bond 0.02841 / 2.03 ( 149) hydrogen bonds : angle 5.46756 / 3.73 ( 372) glycosidic custom : bond 0.00066 / 0.03 ( 1) glycosidic custom : angle 0.90190 / 0.48 ( 3) link_ALPHA1-3 : bond 0.00316 / 0.17 ( 1) link_ALPHA1-3 : angle 3.29951 / 1.73 ( 3) link_ALPHA1-6 : bond 0.00738 / 0.39 ( 1) link_ALPHA1-6 : angle 1.25042 / 0.70 ( 3) link_BETA1-4 : bond 0.00152 / 0.08 ( 2) link_BETA1-4 : angle 2.31629 / 1.70 ( 6) link_BETA1-6 : bond 0.00544 / 0.29 ( 1) link_BETA1-6 : angle 1.00617 / 0.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.180 Fit side-chains REVERT: A 55 SER cc_start: 0.8988 (m) cc_final: 0.8604 (p) REVERT: A 136 MET cc_start: 0.5711 (ttt) cc_final: 0.3446 (mtp) REVERT: A 164 GLN cc_start: 0.8322 (mp10) cc_final: 0.7238 (tt0) REVERT: A 187 MET cc_start: 0.8378 (ptp) cc_final: 0.7794 (ppp) REVERT: A 268 LYS cc_start: 0.8407 (tttp) cc_final: 0.8054 (ttmm) REVERT: A 271 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7665 (t70) REVERT: B 97 GLN cc_start: 0.8128 (mm110) cc_final: 0.7658 (mm110) REVERT: B 162 ASP cc_start: 0.9292 (m-30) cc_final: 0.8946 (m-30) REVERT: B 206 GLN cc_start: 0.8185 (mp10) cc_final: 0.7864 (mp-120) REVERT: C 48 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8727 (mt0) REVERT: C 98 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8262 (mt) REVERT: C 124 MET cc_start: 0.8693 (mmm) cc_final: 0.8334 (mmt) REVERT: C 212 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8689 (mp) outliers start: 21 outliers final: 16 residues processed: 104 average time/residue: 0.4359 time to fit residues: 47.6511 Evaluate side-chains 111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 48 GLN Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 79 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 = 0.3415 r_free = 0.3415 target = 0.123814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.098372 restraints weight = 8095.345| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.11 r_work: 0.2977 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6139 Z= 0.139 Angle : 0.520 8.749 8374 Z= 0.259 Chirality : 0.042 0.187 953 Planarity : 0.004 0.032 1065 Dihedral : 6.868 72.454 980 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.24 % Allowed : 23.46 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.57 (0.29), residues: 741 helix: -1.79 (0.67), residues: 54 sheet: 0.23 (0.38), residues: 181 loop : -0.42 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 41 TYR 0.011 0.001 TYR D 37 PHE 0.009 0.001 PHE C 157 TRP 0.008 0.001 TRP C 155 HIS 0.002 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 6133) covalent geometry : angle 0.51267 / 0.26 ( 8356) hydrogen bonds : bond 0.02579 / 1.85 ( 149) hydrogen bonds : angle 5.39374 / 3.68 ( 372) glycosidic custom : bond 0.00185 / 0.10 ( 1) glycosidic custom : angle 0.77296 / 0.41 ( 3) link_ALPHA1-3 : bond 0.00317 / 0.17 ( 1) link_ALPHA1-3 : angle 3.32192 / 1.74 ( 3) link_ALPHA1-6 : bond 0.00768 / 0.40 ( 1) link_ALPHA1-6 : angle 1.25871 / 0.70 ( 3) link_BETA1-4 : bond 0.00139 / 0.07 ( 2) link_BETA1-4 : angle 2.16759 / 1.62 ( 6) link_BETA1-6 : bond 0.00541 / 0.28 ( 1) link_BETA1-6 : angle 1.13517 / 0.59 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.138 Fit side-chains REVERT: A 55 SER cc_start: 0.8937 (m) cc_final: 0.8579 (p) REVERT: A 136 MET cc_start: 0.5739 (ttt) cc_final: 0.3506 (mtp) REVERT: A 164 GLN cc_start: 0.8318 (mp10) cc_final: 0.7265 (tt0) REVERT: A 187 MET cc_start: 0.8136 (ptp) cc_final: 0.7684 (ppp) REVERT: A 268 LYS cc_start: 0.8447 (tttp) cc_final: 0.8070 (ttmt) REVERT: A 271 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7674 (t70) REVERT: B 97 GLN cc_start: 0.8122 (mm110) cc_final: 0.7698 (mm110) REVERT: B 162 ASP cc_start: 0.9229 (m-30) cc_final: 0.8895 (m-30) REVERT: C 48 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8778 (mt0) REVERT: C 124 MET cc_start: 0.8749 (mmm) cc_final: 0.8422 (mmt) REVERT: C 212 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8705 (mt) outliers start: 21 outliers final: 15 residues processed: 104 average time/residue: 0.3856 time to fit residues: 42.1005 Evaluate side-chains 108 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 48 GLN Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 0.0050 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 61 optimal weight: 8.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.101538 restraints weight = 8054.337| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.11 r_work: 0.3053 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6139 Z= 0.087 Angle : 0.490 8.504 8374 Z= 0.243 Chirality : 0.041 0.181 953 Planarity : 0.004 0.030 1065 Dihedral : 6.656 69.694 980 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.47 % Allowed : 24.54 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.44 (0.30), residues: 741 helix: -1.80 (0.67), residues: 55 sheet: 0.34 (0.39), residues: 181 loop : -0.31 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 41 TYR 0.013 0.001 TYR D 37 PHE 0.008 0.001 PHE B 173 TRP 0.009 0.001 TRP C 155 HIS 0.002 0.000 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 ( 6133) covalent geometry : angle 0.48188 / 0.24 ( 8356) hydrogen bonds : bond 0.02282 / 1.66 ( 149) hydrogen bonds : angle 5.17984 / 3.53 ( 372) glycosidic custom : bond 0.00257 / 0.14 ( 1) glycosidic custom : angle 0.65083 / 0.35 ( 3) link_ALPHA1-3 : bond 0.00371 / 0.20 ( 1) link_ALPHA1-3 : angle 3.30486 / 1.74 ( 3) link_ALPHA1-6 : bond 0.00731 / 0.38 ( 1) link_ALPHA1-6 : angle 1.28416 / 0.71 ( 3) link_BETA1-4 : bond 0.00221 / 0.11 ( 2) link_BETA1-4 : angle 2.03920 / 1.53 ( 6) link_BETA1-6 : bond 0.00483 / 0.25 ( 1) link_BETA1-6 : angle 1.16574 / 0.61 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1788.80 seconds wall clock time: 31 minutes 12.34 seconds (1872.34 seconds total)