Starting phenix.real_space_refine on Thu Jul 2 03:03:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxo_36707/07_2026/8jxo_36707_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxo_36707/07_2026/8jxo_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_36707/07_2026/8jxo_36707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxo_36707/07_2026/8jxo_36707.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxo_36707/07_2026/8jxo_36707_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxo_36707/07_2026/8jxo_36707_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 20 Ad-hoc single atom residues: {' K': 6} Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Chain breaks: 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: D, E Time building chain proxies: 1.45, per 1000 atoms: 0.23 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: 0.59 Conformation dependent library (CDL) restraints added in 302.6 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: 0.15 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: 0.93 Time building geometry restraints manager: 0.72 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 3.990 nonbonded pdb=" CG MET D 239 " pdb=" K K D 402 " model vdw 1.645 3.990 nonbonded pdb=" CG MET E 239 " pdb=" K K E 402 " model vdw 1.645 3.990 nonbonded pdb=" CB MET E 239 " pdb=" K K E 402 " model vdw 1.890 3.990 nonbonded pdb=" CB MET A 239 " pdb=" K K A 402 " model vdw 1.890 3.990 ... (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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' } 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: 16.510 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: 0.380 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.950 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 6468 Z= 0.644 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (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 ARG 0.002 0.001 ARG A 176 TYR 0.010 0.002 TYR D 102 PHE 0.036 0.003 PHE A 143 TRP 0.011 0.002 TRP E 219 HIS 0.005 0.002 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00867 / 0.63 ( 6465) covalent geometry : angle 1.32574 / 0.90 ( 8826) hydrogen bonds : bond 0.16354 / 11.11 ( 456) hydrogen bonds : angle 6.48797 / 4.68 ( 1341) Misc. bond : bond 0.05191 / 2.60 ( 3) *********************** 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 : 0.249 Fit side-chains REVERT: A 13 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7002 (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: 0.7034 (mp0) outliers start: 156 outliers final: 13 residues processed: 240 average time/residue: 0.3944 time to fit residues: 100.5125 Evaluate side-chains 103 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN A 87 ASN A 98 ASN A 258 GLN D 24 ASN D 87 ASN D 258 GLN E 24 ASN E 87 ASN E 98 ASN E 258 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.142098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122388 restraints weight = 6215.736| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.40 r_work: 0.3494 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6468 Z= 0.159 Angle : 0.627 8.370 8826 Z= 0.325 Chirality : 0.040 0.130 954 Planarity : 0.006 0.078 1095 Dihedral : 9.848 70.864 907 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.77 % Allowed : 3.85 % Favored : 95.38 % Rotamer: Outliers : 6.73 % Allowed : 20.66 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.29), residues: 780 helix: 1.28 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -0.84 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 150 TYR 0.014 0.002 TYR A 86 PHE 0.011 0.001 PHE A 195 TRP 0.013 0.001 TRP E 184 HIS 0.005 0.002 HIS E 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 6465) covalent geometry : angle 0.62686 / 0.33 ( 8826) hydrogen bonds : bond 0.04811 / 3.35 ( 456) hydrogen bonds : angle 4.16520 / 3.05 ( 1341) Misc. bond : bond 0.00111 / 0.06 ( 3) *********************** 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 119 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 76 time to evaluate : 0.239 Fit side-chains REVERT: A 13 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: D 13 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: D 243 ARG cc_start: 0.7459 (ttp-110) cc_final: 0.7256 (ttp80) REVERT: D 260 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7028 (ttpp) REVERT: E 13 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: E 75 MET cc_start: 0.8579 (mtt) cc_final: 0.8303 (mtt) REVERT: E 243 ARG cc_start: 0.7465 (ttp-110) cc_final: 0.7254 (ttp80) REVERT: E 260 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7043 (ttpp) outliers start: 43 outliers final: 16 residues processed: 113 average time/residue: 0.4365 time to fit residues: 52.3098 Evaluate side-chains 97 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 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 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 194 PHE 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 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112527 restraints weight = 6229.243| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.42 r_work: 0.3340 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6468 Z= 0.226 Angle : 0.654 10.438 8826 Z= 0.329 Chirality : 0.042 0.121 954 Planarity : 0.006 0.057 1095 Dihedral : 9.398 78.474 894 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.77 % Allowed : 3.72 % Favored : 95.51 % Rotamer: Outliers : 5.79 % Allowed : 18.94 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.29), residues: 780 helix: 1.82 (0.20), residues: 567 sheet: None (None), residues: 0 loop : 0.09 (0.47), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 51 TYR 0.017 0.002 TYR D 86 PHE 0.017 0.002 PHE D 78 TRP 0.015 0.002 TRP E 219 HIS 0.007 0.002 HIS D 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 ( 6465) covalent geometry : angle 0.65402 / 0.33 ( 8826) hydrogen bonds : bond 0.05229 / 3.62 ( 456) hydrogen bonds : angle 4.06599 / 2.97 ( 1341) Misc. bond : bond 0.00155 / 0.08 ( 3) *********************** 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 110 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 0.244 Fit side-chains REVERT: A 13 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: A 56 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: A 228 ASP cc_start: 0.8606 (m-30) cc_final: 0.8300 (m-30) REVERT: D 13 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: D 56 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7052 (pm20) REVERT: D 203 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7961 (tt) REVERT: D 228 ASP cc_start: 0.8647 (m-30) cc_final: 0.8352 (m-30) REVERT: D 243 ARG cc_start: 0.7456 (ttp-110) cc_final: 0.7227 (ttp80) REVERT: D 260 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7151 (ttpp) REVERT: E 13 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: E 56 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.6991 (pm20) REVERT: E 243 ARG cc_start: 0.7429 (ttp-110) cc_final: 0.7193 (ttp80) REVERT: E 260 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7097 (ttpp) outliers start: 37 outliers final: 18 residues processed: 106 average time/residue: 0.4742 time to fit residues: 53.0239 Evaluate side-chains 95 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 D residue 203 LEU Chi-restraints excluded: chain D residue 260 LYS 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 Chi-restraints excluded: chain E residue 194 PHE 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 69 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.0020 chunk 17 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.137349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116139 restraints weight = 6138.138| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.46 r_work: 0.3378 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6468 Z= 0.137 Angle : 0.549 9.760 8826 Z= 0.274 Chirality : 0.038 0.113 954 Planarity : 0.005 0.048 1095 Dihedral : 8.814 78.865 894 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.95 % Favored : 96.67 % Rotamer: Outliers : 5.32 % Allowed : 18.78 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.30), residues: 780 helix: 2.25 (0.21), residues: 564 sheet: None (None), residues: 0 loop : 0.12 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.013 0.001 TYR D 86 PHE 0.009 0.001 PHE D 195 TRP 0.011 0.001 TRP E 184 HIS 0.003 0.002 HIS E 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 6465) covalent geometry : angle 0.54865 / 0.27 ( 8826) hydrogen bonds : bond 0.04383 / 3.04 ( 456) hydrogen bonds : angle 3.90265 / 2.85 ( 1341) Misc. bond : bond 0.00029 / 0.01 ( 3) *********************** 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 109 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.223 Fit side-chains REVERT: A 13 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: A 56 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.6966 (pm20) REVERT: A 61 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: A 228 ASP cc_start: 0.8353 (m-30) cc_final: 0.8073 (m-30) REVERT: D 13 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: D 228 ASP cc_start: 0.8376 (m-30) cc_final: 0.8113 (m-30) REVERT: D 243 ARG cc_start: 0.7310 (ttp-110) cc_final: 0.7016 (ttp80) REVERT: E 13 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: E 61 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: E 228 ASP cc_start: 0.8362 (m-30) cc_final: 0.8065 (m-30) REVERT: E 243 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6984 (ttp80) REVERT: E 260 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7118 (ttpp) outliers start: 34 outliers final: 15 residues processed: 108 average time/residue: 0.4701 time to fit residues: 53.5253 Evaluate side-chains 90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 194 PHE 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 64 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN D 87 ASN E 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115767 restraints weight = 6249.924| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.49 r_work: 0.3373 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6468 Z= 0.137 Angle : 0.549 9.768 8826 Z= 0.271 Chirality : 0.038 0.114 954 Planarity : 0.005 0.044 1095 Dihedral : 8.579 81.119 891 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.08 % Favored : 96.54 % Rotamer: Outliers : 5.32 % Allowed : 19.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.30), residues: 780 helix: 2.44 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.30 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 243 TYR 0.011 0.001 TYR D 86 PHE 0.009 0.001 PHE D 195 TRP 0.011 0.001 TRP E 184 HIS 0.004 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 6465) covalent geometry : angle 0.54916 / 0.27 ( 8826) hydrogen bonds : bond 0.04354 / 3.01 ( 456) hydrogen bonds : angle 3.85779 / 2.81 ( 1341) Misc. bond : bond 0.00027 / 0.01 ( 3) *********************** 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 101 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 0.169 Fit side-chains REVERT: A 13 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: A 56 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: A 228 ASP cc_start: 0.8366 (m-30) cc_final: 0.8089 (m-30) REVERT: D 13 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: D 228 ASP cc_start: 0.8385 (m-30) cc_final: 0.8130 (m-30) REVERT: D 243 ARG cc_start: 0.7337 (ttp-110) cc_final: 0.7038 (ttp80) REVERT: E 13 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: E 61 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: E 228 ASP cc_start: 0.8393 (m-30) cc_final: 0.8125 (m-30) REVERT: E 243 ARG cc_start: 0.7278 (ttp-110) cc_final: 0.6984 (ttp80) REVERT: E 260 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7180 (ttpp) outliers start: 34 outliers final: 12 residues processed: 97 average time/residue: 0.4955 time to fit residues: 50.6940 Evaluate side-chains 88 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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 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 75 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.130814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108982 restraints weight = 6292.473| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.50 r_work: 0.3309 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 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 : 0.006 0.042 6468 Z= 0.242 Angle : 0.657 12.124 8826 Z= 0.321 Chirality : 0.043 0.125 954 Planarity : 0.005 0.041 1095 Dihedral : 8.588 85.384 882 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.77 % Allowed : 2.82 % Favored : 96.41 % Rotamer: Outliers : 5.63 % Allowed : 19.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.29), residues: 780 helix: 2.09 (0.20), residues: 567 sheet: None (None), residues: 0 loop : 0.30 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.013 0.002 TYR E 76 PHE 0.016 0.002 PHE A 78 TRP 0.013 0.002 TRP E 184 HIS 0.007 0.002 HIS D 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.24 ( 6465) covalent geometry : angle 0.65682 / 0.32 ( 8826) hydrogen bonds : bond 0.05124 / 3.53 ( 456) hydrogen bonds : angle 3.99214 / 2.91 ( 1341) Misc. bond : bond 0.00082 / 0.04 ( 3) *********************** 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 104 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.244 Fit side-chains REVERT: A 13 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: A 56 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7039 (pm20) REVERT: A 228 ASP cc_start: 0.8661 (m-30) cc_final: 0.8391 (m-30) REVERT: D 13 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: D 56 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7173 (pm20) REVERT: D 203 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8002 (tt) REVERT: D 228 ASP cc_start: 0.8717 (m-30) cc_final: 0.8453 (m-30) REVERT: D 243 ARG cc_start: 0.7530 (ttp-110) cc_final: 0.7245 (ttp80) REVERT: D 260 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7291 (ttpp) REVERT: E 13 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: E 203 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8020 (tt) REVERT: E 228 ASP cc_start: 0.8734 (m-30) cc_final: 0.8461 (m-30) REVERT: E 243 ARG cc_start: 0.7503 (ttp-110) cc_final: 0.7227 (ttp80) REVERT: E 260 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7251 (ttpp) outliers start: 36 outliers final: 16 residues processed: 100 average time/residue: 0.4761 time to fit residues: 50.2638 Evaluate side-chains 92 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.136912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115396 restraints weight = 6120.032| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.47 r_work: 0.3370 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6468 Z= 0.130 Angle : 0.550 10.380 8826 Z= 0.269 Chirality : 0.039 0.116 954 Planarity : 0.005 0.040 1095 Dihedral : 8.010 82.021 882 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.33 % Favored : 96.28 % Rotamer: Outliers : 4.54 % Allowed : 20.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.29), residues: 780 helix: 2.38 (0.20), residues: 564 sheet: None (None), residues: 0 loop : 0.22 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.012 0.001 TYR A 86 PHE 0.009 0.001 PHE A 95 TRP 0.010 0.001 TRP E 184 HIS 0.003 0.001 HIS D 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6465) covalent geometry : angle 0.55012 / 0.27 ( 8826) hydrogen bonds : bond 0.04290 / 2.97 ( 456) hydrogen bonds : angle 3.85932 / 2.80 ( 1341) Misc. bond : bond 0.00018 / 0.01 ( 3) *********************** 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 93 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.237 Fit side-chains REVERT: A 13 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: A 228 ASP cc_start: 0.8381 (m-30) cc_final: 0.8112 (m-30) REVERT: D 13 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: D 203 LEU cc_start: 0.8512 (mp) cc_final: 0.7888 (tt) REVERT: D 228 ASP cc_start: 0.8410 (m-30) cc_final: 0.8165 (m-30) REVERT: D 243 ARG cc_start: 0.7389 (ttp-110) cc_final: 0.7066 (ttp80) REVERT: D 260 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7298 (ttpp) REVERT: E 13 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: E 56 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7083 (pm20) REVERT: E 61 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: E 228 ASP cc_start: 0.8431 (m-30) cc_final: 0.8170 (m-30) REVERT: E 243 ARG cc_start: 0.7341 (ttp-110) cc_final: 0.7025 (ttp80) REVERT: E 260 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7276 (ttpp) outliers start: 29 outliers final: 15 residues processed: 93 average time/residue: 0.4957 time to fit residues: 48.5969 Evaluate side-chains 86 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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 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 260 LYS 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 Chi-restraints excluded: chain E residue 194 PHE Chi-restraints excluded: chain E residue 260 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3597 r_free = 0.3597 target = 0.133539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112036 restraints weight = 6217.786| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.47 r_work: 0.3328 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6468 Z= 0.184 Angle : 0.603 11.993 8826 Z= 0.292 Chirality : 0.041 0.120 954 Planarity : 0.005 0.039 1095 Dihedral : 8.279 84.227 882 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.21 % Favored : 96.41 % Rotamer: Outliers : 4.38 % Allowed : 21.28 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.29), residues: 780 helix: 2.29 (0.20), residues: 567 sheet: None (None), residues: 0 loop : 0.36 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.011 0.002 TYR A 86 PHE 0.012 0.002 PHE A 95 TRP 0.012 0.001 TRP E 184 HIS 0.005 0.002 HIS D 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 ( 6465) covalent geometry : angle 0.60337 / 0.29 ( 8826) hydrogen bonds : bond 0.04677 / 3.23 ( 456) hydrogen bonds : angle 3.89548 / 2.83 ( 1341) Misc. bond : bond 0.00050 / 0.03 ( 3) *********************** 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 93 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.248 Fit side-chains REVERT: A 13 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: A 228 ASP cc_start: 0.8544 (m-30) cc_final: 0.8277 (m-30) REVERT: D 13 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: D 203 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7906 (tt) REVERT: D 228 ASP cc_start: 0.8588 (m-30) cc_final: 0.8325 (m-30) REVERT: D 243 ARG cc_start: 0.7439 (ttp-110) cc_final: 0.7154 (ttp80) REVERT: D 260 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7340 (ttpp) REVERT: E 13 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: E 56 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7082 (pm20) REVERT: E 61 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: E 203 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7916 (tt) REVERT: E 228 ASP cc_start: 0.8591 (m-30) cc_final: 0.8331 (m-30) REVERT: E 243 ARG cc_start: 0.7388 (ttp-110) cc_final: 0.7044 (ttp80) REVERT: E 260 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7292 (ttpp) outliers start: 28 outliers final: 15 residues processed: 90 average time/residue: 0.4744 time to fit residues: 45.1211 Evaluate side-chains 89 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 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 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 D residue 260 LYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.135807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113721 restraints weight = 5998.587| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.49 r_work: 0.3377 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6468 Z= 0.129 Angle : 0.548 10.572 8826 Z= 0.266 Chirality : 0.039 0.116 954 Planarity : 0.005 0.039 1095 Dihedral : 7.845 81.326 882 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.59 % Favored : 96.03 % Rotamer: Outliers : 3.76 % Allowed : 22.22 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.29), residues: 780 helix: 2.50 (0.20), residues: 564 sheet: None (None), residues: 0 loop : 0.31 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.012 0.001 TYR A 86 PHE 0.012 0.001 PHE A 95 TRP 0.010 0.001 TRP E 184 HIS 0.003 0.001 HIS D 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 6465) covalent geometry : angle 0.54797 / 0.27 ( 8826) hydrogen bonds : bond 0.04239 / 2.93 ( 456) hydrogen bonds : angle 3.83316 / 2.78 ( 1341) Misc. bond : bond 0.00016 / 0.01 ( 3) *********************** 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 90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.251 Fit side-chains REVERT: A 228 ASP cc_start: 0.8366 (m-30) cc_final: 0.8114 (m-30) REVERT: D 13 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: D 203 LEU cc_start: 0.8622 (mp) cc_final: 0.8383 (mm) REVERT: D 228 ASP cc_start: 0.8398 (m-30) cc_final: 0.8167 (m-30) REVERT: D 243 ARG cc_start: 0.7493 (ttp-110) cc_final: 0.7173 (ttp80) REVERT: D 260 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7379 (ttpp) REVERT: E 203 LEU cc_start: 0.8618 (mp) cc_final: 0.8374 (mm) REVERT: E 228 ASP cc_start: 0.8422 (m-30) cc_final: 0.8175 (m-30) REVERT: E 243 ARG cc_start: 0.7439 (ttp-110) cc_final: 0.7133 (ttp80) REVERT: E 260 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7348 (ttpp) outliers start: 24 outliers final: 14 residues processed: 88 average time/residue: 0.5154 time to fit residues: 47.8411 Evaluate side-chains 85 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 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 D residue 260 LYS 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 260 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.135788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114404 restraints weight = 6078.288| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.45 r_work: 0.3329 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6468 Z= 0.146 Angle : 0.568 11.290 8826 Z= 0.275 Chirality : 0.039 0.114 954 Planarity : 0.005 0.039 1095 Dihedral : 7.069 83.115 873 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.08 % Favored : 96.54 % Rotamer: Outliers : 3.29 % Allowed : 22.38 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.29), residues: 780 helix: 2.45 (0.20), residues: 567 sheet: None (None), residues: 0 loop : 0.46 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.011 0.001 TYR A 86 PHE 0.014 0.001 PHE A 95 TRP 0.011 0.001 TRP E 184 HIS 0.004 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 6465) covalent geometry : angle 0.56801 / 0.28 ( 8826) hydrogen bonds : bond 0.04376 / 3.02 ( 456) hydrogen bonds : angle 3.83542 / 2.79 ( 1341) Misc. bond : bond 0.00029 / 0.01 ( 3) ********************** 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 89 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.242 Fit side-chains REVERT: A 13 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: A 203 LEU cc_start: 0.8392 (mp) cc_final: 0.8137 (mm) REVERT: A 228 ASP cc_start: 0.8370 (m-30) cc_final: 0.8104 (m-30) REVERT: D 13 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: D 203 LEU cc_start: 0.8419 (mp) cc_final: 0.8164 (mm) REVERT: D 228 ASP cc_start: 0.8399 (m-30) cc_final: 0.8148 (m-30) REVERT: D 243 ARG cc_start: 0.7303 (ttp-110) cc_final: 0.6945 (ttp80) REVERT: D 260 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7330 (ttpp) REVERT: E 203 LEU cc_start: 0.8424 (mp) cc_final: 0.8165 (mm) REVERT: E 228 ASP cc_start: 0.8414 (m-30) cc_final: 0.8154 (m-30) REVERT: E 243 ARG cc_start: 0.7252 (ttp-110) cc_final: 0.6910 (ttp80) REVERT: E 260 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7326 (ttpp) outliers start: 21 outliers final: 10 residues processed: 87 average time/residue: 0.4761 time to fit residues: 43.7845 Evaluate side-chains 83 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 D residue 260 LYS Chi-restraints excluded: chain E residue 65 SER 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 260 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.137016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115470 restraints weight = 6176.652| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.47 r_work: 0.3370 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6468 Z= 0.134 Angle : 0.557 10.817 8826 Z= 0.269 Chirality : 0.039 0.114 954 Planarity : 0.005 0.039 1095 Dihedral : 6.964 82.518 873 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.33 % Favored : 96.28 % Rotamer: Outliers : 2.66 % Allowed : 22.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.29), residues: 780 helix: 2.55 (0.20), residues: 564 sheet: None (None), residues: 0 loop : 0.37 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.012 0.001 TYR A 86 PHE 0.015 0.001 PHE A 95 TRP 0.011 0.001 TRP A 184 HIS 0.003 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6465) covalent geometry : angle 0.55686 / 0.27 ( 8826) hydrogen bonds : bond 0.04259 / 2.94 ( 456) hydrogen bonds : angle 3.81737 / 2.77 ( 1341) Misc. bond : bond 0.00020 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2673.40 seconds wall clock time: 46 minutes 30.40 seconds (2790.40 seconds total)