Starting phenix.real_space_refine on Tue Mar 11 15:26:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxo_36707/03_2025/8jxo_36707_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxo_36707/03_2025/8jxo_36707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxo_36707/03_2025/8jxo_36707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxo_36707/03_2025/8jxo_36707.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxo_36707/03_2025/8jxo_36707_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxo_36707/03_2025/8jxo_36707_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 K 18 8.98 5 S 42 5.16 5 C 4176 2.51 5 N 954 2.21 5 O 1104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6294 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2069 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 26 Unusual residues: {' K': 6, 'RET': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 518 SG CYS A 72 43.541 52.990 56.049 1.00 30.00 S Restraints were copied for chains: E, D Time building chain proxies: 10.00, per 1000 atoms: 1.59 Number of scatterers: 6294 At special positions: 0 Unit cell: (73.85, 73.15, 90.3, 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) K 18 19.00 S 42 16.00 O 1104 8.00 N 954 7.00 C 4176 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 863.7 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 81.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 Processing helix chain 'A' and resid 17 through 45 Processing helix chain 'A' and resid 59 through 62 Processing helix chain 'A' and resid 63 through 89 Processing helix chain 'A' and resid 103 through 120 removed outlier: 4.483A pdb=" N ILE A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.830A pdb=" N VAL A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 174 removed outlier: 3.626A pdb=" N TYR A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 152 " --> pdb=" O PRO A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.826A pdb=" N TRP A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.587A pdb=" N PHE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Proline residue: A 202 - end of helix removed outlier: 3.533A pdb=" N TRP A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.534A pdb=" N ILE A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 263 Processing helix chain 'D' and resid 8 through 12 Processing helix chain 'D' and resid 17 through 45 Processing helix chain 'D' and resid 59 through 62 Processing helix chain 'D' and resid 63 through 89 Processing helix chain 'D' and resid 103 through 120 removed outlier: 4.483A pdb=" N ILE D 107 " --> pdb=" O SER D 103 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 124 through 145 removed outlier: 3.830A pdb=" N VAL D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 174 removed outlier: 3.626A pdb=" N TYR D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 152 " --> pdb=" O PRO D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.826A pdb=" N TRP D 185 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 205 removed outlier: 3.587A pdb=" N PHE D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Proline residue: D 202 - end of helix removed outlier: 3.532A pdb=" N TRP D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 216 through 231 removed outlier: 3.534A pdb=" N ILE D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 263 Processing helix chain 'E' and resid 8 through 12 Processing helix chain 'E' and resid 17 through 45 Processing helix chain 'E' and resid 59 through 62 Processing helix chain 'E' and resid 63 through 89 Processing helix chain 'E' and resid 103 through 120 removed outlier: 4.483A pdb=" N ILE E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 124 through 145 removed outlier: 3.829A pdb=" N VAL E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE E 143 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 174 removed outlier: 3.626A pdb=" N TYR E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR E 152 " --> pdb=" O PRO E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 196 removed outlier: 3.826A pdb=" N TRP E 185 " --> pdb=" O ASP E 181 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR E 186 " --> pdb=" O SER E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 205 removed outlier: 3.587A pdb=" N PHE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Proline residue: E 202 - end of helix removed outlier: 3.532A pdb=" N TRP E 205 " --> pdb=" O PHE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 216 through 231 removed outlier: 3.534A pdb=" N ILE E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 263 456 hydrogen bonds defined for protein. 1341 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: 1.93 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 980 1.32 - 1.44: 1939 1.44 - 1.56: 3492 1.56 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 6465 Sorted by residual: bond pdb=" CA LEU D 192 " pdb=" C LEU D 192 " ideal model delta sigma weight residual 1.524 1.472 0.053 1.24e-02 6.50e+03 1.80e+01 bond pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 1.524 1.472 0.053 1.24e-02 6.50e+03 1.80e+01 bond pdb=" CA LEU E 192 " pdb=" C LEU E 192 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.24e-02 6.50e+03 1.79e+01 bond pdb=" C ASP A 82 " pdb=" O ASP A 82 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.17e-02 7.31e+03 1.34e+01 bond pdb=" C ASP D 82 " pdb=" O ASP D 82 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.17e-02 7.31e+03 1.34e+01 ... (remaining 6460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 8322 2.42 - 4.84: 407 4.84 - 7.25: 46 7.25 - 9.67: 39 9.67 - 12.09: 12 Bond angle restraints: 8826 Sorted by residual: angle pdb=" N ALA E 137 " pdb=" CA ALA E 137 " pdb=" C ALA E 137 " ideal model delta sigma weight residual 113.41 101.85 11.56 1.22e+00 6.72e-01 8.99e+01 angle pdb=" N ALA A 137 " pdb=" CA ALA A 137 " pdb=" C ALA A 137 " ideal model delta sigma weight residual 113.41 101.85 11.56 1.22e+00 6.72e-01 8.98e+01 angle pdb=" N ALA D 137 " pdb=" CA ALA D 137 " pdb=" C ALA D 137 " ideal model delta sigma weight residual 113.41 101.87 11.54 1.22e+00 6.72e-01 8.94e+01 angle pdb=" N LEU D 192 " pdb=" CA LEU D 192 " pdb=" C LEU D 192 " ideal model delta sigma weight residual 110.97 100.70 10.27 1.09e+00 8.42e-01 8.88e+01 angle pdb=" N LEU A 192 " pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 110.97 100.71 10.26 1.09e+00 8.42e-01 8.87e+01 ... (remaining 8821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 2925 17.05 - 34.10: 393 34.10 - 51.15: 216 51.15 - 68.19: 96 68.19 - 85.24: 15 Dihedral angle restraints: 3645 sinusoidal: 1371 harmonic: 2274 Sorted by residual: dihedral pdb=" C ALA E 147 " pdb=" N ALA E 147 " pdb=" CA ALA E 147 " pdb=" CB ALA E 147 " ideal model delta harmonic sigma weight residual -122.60 -134.59 11.99 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" C ALA D 147 " pdb=" N ALA D 147 " pdb=" CA ALA D 147 " pdb=" CB ALA D 147 " ideal model delta harmonic sigma weight residual -122.60 -134.59 11.99 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" C ALA A 147 " pdb=" N ALA A 147 " pdb=" CA ALA A 147 " pdb=" CB ALA A 147 " ideal model delta harmonic sigma weight residual -122.60 -134.57 11.97 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 3642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 803 0.111 - 0.222: 115 0.222 - 0.332: 24 0.332 - 0.443: 6 0.443 - 0.554: 6 Chirality restraints: 954 Sorted by residual: chirality pdb=" CA ALA D 147 " pdb=" N ALA D 147 " pdb=" C ALA D 147 " pdb=" CB ALA D 147 " both_signs ideal model delta sigma weight residual False 2.48 1.93 0.55 2.00e-01 2.50e+01 7.67e+00 chirality pdb=" CA ALA E 147 " pdb=" N ALA E 147 " pdb=" C ALA E 147 " pdb=" CB ALA E 147 " both_signs ideal model delta sigma weight residual False 2.48 1.93 0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" CA ALA A 147 " pdb=" N ALA A 147 " pdb=" C ALA A 147 " pdb=" CB ALA A 147 " both_signs ideal model delta sigma weight residual False 2.48 1.93 0.55 2.00e-01 2.50e+01 7.65e+00 ... (remaining 951 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 109 " -0.113 5.00e-02 4.00e+02 1.65e-01 4.35e+01 pdb=" N PRO E 110 " 0.285 5.00e-02 4.00e+02 pdb=" CA PRO E 110 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO E 110 " -0.096 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 109 " 0.113 5.00e-02 4.00e+02 1.65e-01 4.35e+01 pdb=" N PRO D 110 " -0.285 5.00e-02 4.00e+02 pdb=" CA PRO D 110 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO D 110 " 0.096 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 109 " 0.113 5.00e-02 4.00e+02 1.65e-01 4.34e+01 pdb=" N PRO A 110 " -0.284 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " 0.096 5.00e-02 4.00e+02 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.34: 12 2.34 - 3.04: 4136 3.04 - 3.74: 12484 3.74 - 4.44: 20815 4.44 - 5.14: 31780 Nonbonded interactions: 69227 Sorted by model distance: nonbonded pdb=" CG MET A 239 " pdb=" K K A 402 " model vdw 1.645 3.250 nonbonded pdb=" CG MET D 239 " pdb=" K K D 402 " model vdw 1.645 3.250 nonbonded pdb=" CG MET E 239 " pdb=" K K E 402 " model vdw 1.645 3.250 nonbonded pdb=" CB MET E 239 " pdb=" K K E 402 " model vdw 1.890 3.250 nonbonded pdb=" CB MET A 239 " pdb=" K K A 402 " model vdw 1.890 3.250 ... (remaining 69222 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' 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 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: 10.990 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: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.940 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 : 0.009 0.053 6465 Z= 0.557 Angle : 1.326 12.088 8826 Z= 0.904 Chirality : 0.095 0.554 954 Planarity : 0.016 0.165 1095 Dihedral : 22.328 85.242 2193 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 1.92 % Allowed : 6.92 % Favored : 91.15 % Rotamer: Outliers : 24.41 % Allowed : 13.15 % Favored : 62.44 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.26), residues: 780 helix: -1.58 (0.17), residues: 555 sheet: None (None), residues: 0 loop : -1.35 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 219 HIS 0.005 0.002 HIS A 210 PHE 0.036 0.003 PHE A 143 TYR 0.010 0.002 TYR D 102 ARG 0.002 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 122 time to evaluate : 0.641 Fit side-chains REVERT: A 13 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: D 13 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: D 86 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: E 13 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7033 (mp0) outliers start: 156 outliers final: 14 residues processed: 240 average time/residue: 0.9116 time to fit residues: 232.1062 Evaluate side-chains 103 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 192 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.0070 chunk 70 optimal weight: 0.6980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 87 ASN A 258 GLN D 24 ASN D 87 ASN D 258 GLN E 24 ASN E 87 ASN E 258 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124865 restraints weight = 6309.434| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.37 r_work: 0.3522 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6465 Z= 0.199 Angle : 0.609 8.063 8826 Z= 0.315 Chirality : 0.040 0.128 954 Planarity : 0.006 0.080 1095 Dihedral : 9.907 69.009 909 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.77 % Allowed : 3.85 % Favored : 95.38 % Rotamer: Outliers : 6.73 % Allowed : 20.34 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.29), residues: 780 helix: 1.14 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -0.93 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 198 HIS 0.004 0.002 HIS A 224 PHE 0.012 0.001 PHE D 195 TYR 0.016 0.002 TYR A 86 ARG 0.001 0.000 ARG E 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 83 time to evaluate : 0.623 Fit side-chains REVERT: A 13 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: D 13 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: D 260 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7009 (ttpp) REVERT: E 13 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: E 75 MET cc_start: 0.8516 (mtt) cc_final: 0.8221 (mtt) REVERT: E 166 TYR cc_start: 0.7712 (t80) cc_final: 0.7491 (t80) REVERT: E 260 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.6994 (ttpp) outliers start: 43 outliers final: 14 residues processed: 120 average time/residue: 0.9469 time to fit residues: 120.6981 Evaluate side-chains 99 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 124 TYR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain E residue 260 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 98 ASN D 53 HIS E 53 HIS E 98 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106821 restraints weight = 6491.233| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.48 r_work: 0.3343 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 6465 Z= 0.497 Angle : 0.749 11.130 8826 Z= 0.373 Chirality : 0.047 0.127 954 Planarity : 0.006 0.054 1095 Dihedral : 9.840 81.935 896 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.77 % Allowed : 3.46 % Favored : 95.77 % Rotamer: Outliers : 5.79 % Allowed : 19.25 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.29), residues: 780 helix: 1.57 (0.20), residues: 564 sheet: None (None), residues: 0 loop : 0.17 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 219 HIS 0.009 0.003 HIS E 224 PHE 0.028 0.003 PHE E 78 TYR 0.020 0.003 TYR D 86 ARG 0.004 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 0.634 Fit side-chains REVERT: A 13 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: A 56 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: A 203 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8231 (tt) REVERT: D 13 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: D 56 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: D 203 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8225 (tt) REVERT: E 13 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: E 203 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8254 (tt) REVERT: E 260 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7268 (ttpp) outliers start: 37 outliers final: 18 residues processed: 107 average time/residue: 1.0431 time to fit residues: 118.0411 Evaluate side-chains 99 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 124 TYR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 194 PHE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 260 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112481 restraints weight = 6387.562| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.51 r_work: 0.3362 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6465 Z= 0.212 Angle : 0.572 9.984 8826 Z= 0.283 Chirality : 0.038 0.114 954 Planarity : 0.005 0.048 1095 Dihedral : 9.270 82.870 896 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.77 % Allowed : 2.95 % Favored : 96.28 % Rotamer: Outliers : 5.32 % Allowed : 19.72 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.29), residues: 780 helix: 2.03 (0.20), residues: 564 sheet: None (None), residues: 0 loop : 0.14 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 184 HIS 0.004 0.002 HIS A 224 PHE 0.009 0.001 PHE D 195 TYR 0.013 0.001 TYR A 86 ARG 0.001 0.000 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.664 Fit side-chains REVERT: A 13 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: A 56 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: A 228 ASP cc_start: 0.8354 (m-30) cc_final: 0.8079 (m-30) REVERT: D 13 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: D 56 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7044 (pm20) REVERT: D 203 LEU cc_start: 0.8325 (mp) cc_final: 0.7711 (tt) REVERT: D 228 ASP cc_start: 0.8378 (m-30) cc_final: 0.8093 (m-30) REVERT: D 243 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7428 (ttp-170) REVERT: E 13 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: E 203 LEU cc_start: 0.8358 (mp) cc_final: 0.7757 (tt) REVERT: E 228 ASP cc_start: 0.8403 (m-30) cc_final: 0.8105 (m-30) REVERT: E 260 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7108 (ttpp) outliers start: 34 outliers final: 17 residues processed: 104 average time/residue: 1.1207 time to fit residues: 122.9040 Evaluate side-chains 91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 124 TYR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 260 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112666 restraints weight = 6318.153| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.51 r_work: 0.3369 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6465 Z= 0.215 Angle : 0.563 9.721 8826 Z= 0.277 Chirality : 0.039 0.114 954 Planarity : 0.005 0.044 1095 Dihedral : 9.056 83.971 896 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.72 % Favored : 95.90 % Rotamer: Outliers : 5.95 % Allowed : 19.25 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.29), residues: 780 helix: 2.23 (0.20), residues: 564 sheet: None (None), residues: 0 loop : 0.22 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 184 HIS 0.004 0.001 HIS D 224 PHE 0.010 0.001 PHE D 95 TYR 0.011 0.001 TYR E 86 ARG 0.002 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 66 time to evaluate : 0.627 Fit side-chains REVERT: A 13 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: A 56 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: A 61 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: A 228 ASP cc_start: 0.8366 (m-30) cc_final: 0.8073 (m-30) REVERT: D 13 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: D 61 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8107 (pm20) REVERT: D 228 ASP cc_start: 0.8384 (m-30) cc_final: 0.8103 (m-30) REVERT: E 13 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: E 61 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8085 (pm20) REVERT: E 228 ASP cc_start: 0.8396 (m-30) cc_final: 0.8102 (m-30) REVERT: E 260 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7134 (ttpp) outliers start: 38 outliers final: 12 residues processed: 95 average time/residue: 1.1214 time to fit residues: 112.4645 Evaluate side-chains 85 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 124 TYR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 194 PHE Chi-restraints excluded: chain E residue 260 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 ASN E 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113620 restraints weight = 6264.464| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.50 r_work: 0.3369 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6465 Z= 0.197 Angle : 0.550 9.903 8826 Z= 0.269 Chirality : 0.038 0.115 954 Planarity : 0.005 0.043 1095 Dihedral : 8.532 84.305 890 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.97 % Favored : 95.64 % Rotamer: Outliers : 4.85 % Allowed : 20.19 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.29), residues: 780 helix: 2.40 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.44 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 184 HIS 0.003 0.001 HIS D 224 PHE 0.009 0.001 PHE A 95 TYR 0.011 0.001 TYR D 86 ARG 0.002 0.000 ARG D 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.633 Fit side-chains REVERT: A 13 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: A 61 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: A 228 ASP cc_start: 0.8380 (m-30) cc_final: 0.8115 (m-30) REVERT: D 13 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: D 228 ASP cc_start: 0.8403 (m-30) cc_final: 0.8136 (m-30) REVERT: D 243 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7648 (tmm160) REVERT: E 13 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: E 56 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: E 61 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: E 228 ASP cc_start: 0.8441 (m-30) cc_final: 0.8177 (m-30) outliers start: 31 outliers final: 13 residues processed: 88 average time/residue: 1.1033 time to fit residues: 102.5578 Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 124 TYR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 182 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113501 restraints weight = 6205.804| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.49 r_work: 0.3369 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6465 Z= 0.201 Angle : 0.558 10.493 8826 Z= 0.270 Chirality : 0.039 0.115 954 Planarity : 0.005 0.043 1095 Dihedral : 8.318 84.654 887 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % Rotamer: Outliers : 4.38 % Allowed : 20.66 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.29), residues: 780 helix: 2.46 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.51 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 184 HIS 0.004 0.001 HIS D 224 PHE 0.011 0.001 PHE A 95 TYR 0.011 0.001 TYR A 86 ARG 0.002 0.000 ARG E 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.689 Fit side-chains REVERT: A 203 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 228 ASP cc_start: 0.8380 (m-30) cc_final: 0.8110 (m-30) REVERT: D 228 ASP cc_start: 0.8409 (m-30) cc_final: 0.8150 (m-30) REVERT: D 243 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7607 (tmm160) REVERT: E 56 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7102 (pm20) REVERT: E 61 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: E 228 ASP cc_start: 0.8452 (m-30) cc_final: 0.8182 (m-30) outliers start: 28 outliers final: 12 residues processed: 87 average time/residue: 1.0422 time to fit residues: 96.1039 Evaluate side-chains 84 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 124 TYR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 182 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN D 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.133855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112890 restraints weight = 6306.384| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.49 r_work: 0.3362 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6465 Z= 0.211 Angle : 0.563 10.728 8826 Z= 0.272 Chirality : 0.039 0.115 954 Planarity : 0.005 0.042 1095 Dihedral : 7.184 85.169 875 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.97 % Favored : 95.64 % Rotamer: Outliers : 4.07 % Allowed : 20.81 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.29), residues: 780 helix: 2.45 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.58 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 184 HIS 0.004 0.001 HIS A 224 PHE 0.012 0.001 PHE A 95 TYR 0.011 0.001 TYR A 86 ARG 0.001 0.000 ARG E 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.705 Fit side-chains REVERT: A 13 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: A 136 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7925 (mm) REVERT: A 203 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8308 (mm) REVERT: A 228 ASP cc_start: 0.8421 (m-30) cc_final: 0.8164 (m-30) REVERT: A 243 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7614 (tmm160) REVERT: D 13 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: D 136 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7868 (mm) REVERT: D 228 ASP cc_start: 0.8445 (m-30) cc_final: 0.8196 (m-30) REVERT: D 243 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7621 (tmm160) REVERT: E 13 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: E 56 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7052 (pm20) REVERT: E 61 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8057 (pm20) REVERT: E 136 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7848 (mm) REVERT: E 228 ASP cc_start: 0.8480 (m-30) cc_final: 0.8221 (m-30) outliers start: 26 outliers final: 8 residues processed: 85 average time/residue: 1.0730 time to fit residues: 96.5479 Evaluate side-chains 86 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 182 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN E 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.113653 restraints weight = 6353.861| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.50 r_work: 0.3368 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6465 Z= 0.193 Angle : 0.552 10.283 8826 Z= 0.267 Chirality : 0.039 0.115 954 Planarity : 0.005 0.043 1095 Dihedral : 7.100 84.071 875 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % Rotamer: Outliers : 2.66 % Allowed : 22.38 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.29), residues: 780 helix: 2.50 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.61 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 184 HIS 0.003 0.001 HIS D 224 PHE 0.013 0.001 PHE A 95 TYR 0.011 0.001 TYR E 86 ARG 0.001 0.000 ARG D 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.810 Fit side-chains REVERT: A 13 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: A 136 LEU cc_start: 0.8154 (mt) cc_final: 0.7924 (mm) REVERT: A 203 LEU cc_start: 0.8547 (mp) cc_final: 0.8314 (mm) REVERT: A 228 ASP cc_start: 0.8369 (m-30) cc_final: 0.8115 (m-30) REVERT: A 243 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7614 (tmm160) REVERT: D 13 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: D 136 LEU cc_start: 0.8103 (mt) cc_final: 0.7869 (mm) REVERT: D 203 LEU cc_start: 0.8566 (mp) cc_final: 0.8324 (mm) REVERT: D 228 ASP cc_start: 0.8402 (m-30) cc_final: 0.8159 (m-30) REVERT: D 243 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7606 (tmm160) REVERT: E 13 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: E 61 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: E 136 LEU cc_start: 0.8102 (mt) cc_final: 0.7850 (mm) REVERT: E 203 LEU cc_start: 0.8579 (mp) cc_final: 0.8333 (mm) REVERT: E 228 ASP cc_start: 0.8435 (m-30) cc_final: 0.8180 (m-30) outliers start: 17 outliers final: 8 residues processed: 78 average time/residue: 1.1277 time to fit residues: 92.9645 Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.0470 chunk 75 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.135628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114990 restraints weight = 6286.453| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.46 r_work: 0.3374 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6465 Z= 0.179 Angle : 0.542 9.783 8826 Z= 0.263 Chirality : 0.038 0.115 954 Planarity : 0.005 0.043 1095 Dihedral : 7.032 83.642 875 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % Rotamer: Outliers : 2.19 % Allowed : 23.00 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.29), residues: 780 helix: 2.57 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.62 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 184 HIS 0.003 0.001 HIS A 224 PHE 0.015 0.001 PHE A 95 TYR 0.011 0.001 TYR E 86 ARG 0.001 0.000 ARG E 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.744 Fit side-chains REVERT: A 13 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: A 203 LEU cc_start: 0.8490 (mp) cc_final: 0.8261 (mm) REVERT: A 228 ASP cc_start: 0.8278 (m-30) cc_final: 0.8025 (m-30) REVERT: D 13 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: D 203 LEU cc_start: 0.8505 (mp) cc_final: 0.8267 (mm) REVERT: D 228 ASP cc_start: 0.8308 (m-30) cc_final: 0.8066 (m-30) REVERT: D 243 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7548 (tmm160) REVERT: E 13 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6631 (mp0) REVERT: E 136 LEU cc_start: 0.8028 (mt) cc_final: 0.7826 (mm) REVERT: E 203 LEU cc_start: 0.8538 (mp) cc_final: 0.8302 (mm) REVERT: E 228 ASP cc_start: 0.8343 (m-30) cc_final: 0.8089 (m-30) outliers start: 14 outliers final: 8 residues processed: 76 average time/residue: 1.0412 time to fit residues: 84.1580 Evaluate side-chains 73 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114164 restraints weight = 6362.102| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.47 r_work: 0.3366 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6465 Z= 0.190 Angle : 0.531 10.038 8826 Z= 0.263 Chirality : 0.038 0.114 954 Planarity : 0.005 0.044 1095 Dihedral : 6.955 85.905 872 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.46 % Favored : 96.15 % Rotamer: Outliers : 2.50 % Allowed : 23.00 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.29), residues: 780 helix: 2.57 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.62 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 184 HIS 0.003 0.001 HIS E 224 PHE 0.017 0.001 PHE A 95 TYR 0.010 0.001 TYR E 86 ARG 0.001 0.000 ARG D 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5683.70 seconds wall clock time: 97 minutes 37.16 seconds (5857.16 seconds total)