Starting phenix.real_space_refine on Tue Feb 11 15:47:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxo_36707/02_2025/8jxo_36707_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxo_36707/02_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_36707/02_2025/8jxo_36707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxo_36707/02_2025/8jxo_36707.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxo_36707/02_2025/8jxo_36707_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxo_36707/02_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-5592/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: 8.14, per 1000 atoms: 1.29 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: 1.57 Conformation dependent library (CDL) restraints added in 920.4 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: 0.49 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: 1.62 Time building geometry restraints manager: 1.79 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: 0.04 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: 22.440 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: 4.270 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:14.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.080 ------------------------------------------------------------------------------- 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 : 0.618 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: 0.9176 time to fit residues: 233.3401 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 : 0.630 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124832 restraints weight = 6309.444| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.37 r_work: 0.3520 rms_B_bonded: 1.72 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: 0.8306 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 : 0.669 Fit side-chains REVERT: A 13 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: D 13 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: D 260 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7026 (ttpp) REVERT: E 13 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: E 75 MET cc_start: 0.8521 (mtt) cc_final: 0.8226 (mtt) REVERT: E 166 TYR cc_start: 0.7716 (t80) cc_final: 0.7496 (t80) REVERT: E 260 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7012 (ttpp) outliers start: 43 outliers final: 14 residues processed: 120 average time/residue: 0.9747 time to fit residues: 123.9430 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 : 0.620 ------------------------------------------------------------------------------- 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: 4.9990 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 = 0.127497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106827 restraints weight = 6486.657| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.48 r_work: 0.3344 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 6465 Z= 0.498 Angle : 0.748 11.162 8826 Z= 0.372 Chirality : 0.047 0.127 954 Planarity : 0.006 0.054 1095 Dihedral : 9.826 81.601 896 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.49 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: 1.58 (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 0.017 0.002 TRP E 219 HIS 0.009 0.003 HIS E 224 PHE 0.027 0.003 PHE D 78 TYR 0.019 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 : 0.639 Fit side-chains REVERT: A 13 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: A 56 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7160 (pm20) REVERT: A 203 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8224 (tt) REVERT: D 13 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: D 56 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: D 203 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8231 (tt) REVERT: E 13 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: E 203 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8251 (tt) REVERT: E 260 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7259 (ttpp) outliers start: 37 outliers final: 18 residues processed: 107 average time/residue: 1.0736 time to fit residues: 121.4551 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 : 0.673 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 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 = 0.3597 r_free = 0.3597 target = 0.133713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112720 restraints weight = 6388.485| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.51 r_work: 0.3365 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6465 Z= 0.217 Angle : 0.572 9.975 8826 Z= 0.283 Chirality : 0.038 0.115 954 Planarity : 0.005 0.047 1095 Dihedral : 9.247 82.590 896 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.77 % Allowed : 3.08 % Favored : 96.15 % Rotamer: Outliers : 5.48 % Allowed : 19.72 % 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: 2.25 (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 107 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.691 Fit side-chains REVERT: A 13 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: A 56 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.6949 (pm20) REVERT: A 228 ASP cc_start: 0.8350 (m-30) cc_final: 0.8052 (m-30) REVERT: D 13 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: D 56 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7036 (pm20) REVERT: D 203 LEU cc_start: 0.8317 (mp) cc_final: 0.7702 (tt) REVERT: D 228 ASP cc_start: 0.8356 (m-30) cc_final: 0.8066 (m-30) REVERT: D 243 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7422 (ttp-170) REVERT: E 13 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: E 203 LEU cc_start: 0.8347 (mp) cc_final: 0.7742 (tt) REVERT: E 228 ASP cc_start: 0.8403 (m-30) cc_final: 0.8112 (m-30) REVERT: E 260 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7103 (ttpp) outliers start: 35 outliers final: 17 residues processed: 104 average time/residue: 1.2258 time to fit residues: 134.0611 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 : 0.680 ------------------------------------------------------------------------------- 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: 9.9990 chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.134103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113039 restraints weight = 6306.109| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.51 r_work: 0.3360 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6465 Z= 0.207 Angle : 0.559 9.621 8826 Z= 0.275 Chirality : 0.038 0.114 954 Planarity : 0.005 0.044 1095 Dihedral : 9.017 83.509 896 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % 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: 2.69 (0.29), residues: 780 helix: 2.31 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.38 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 184 HIS 0.003 0.001 HIS A 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 102 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 0.628 Fit side-chains REVERT: A 13 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: A 56 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: A 61 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: A 228 ASP cc_start: 0.8427 (m-30) cc_final: 0.8154 (m-30) REVERT: D 13 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: D 228 ASP cc_start: 0.8447 (m-30) cc_final: 0.8185 (m-30) REVERT: E 13 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: E 61 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: E 228 ASP cc_start: 0.8483 (m-30) cc_final: 0.8205 (m-30) REVERT: E 260 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7219 (ttpp) outliers start: 34 outliers final: 12 residues processed: 95 average time/residue: 1.1144 time to fit residues: 111.6519 Evaluate side-chains 86 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 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 = 0.3608 r_free = 0.3608 target = 0.134618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113610 restraints weight = 6265.062| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.50 r_work: 0.3370 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: 0.8337 moved from start: 0.4048 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= 0.198 Angle : 0.550 9.939 8826 Z= 0.269 Chirality : 0.038 0.115 954 Planarity : 0.005 0.043 1095 Dihedral : 8.392 84.356 887 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % Rotamer: Outliers : 5.01 % Allowed : 19.72 % 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 (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: 2.41 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.40 (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 A 224 PHE 0.010 0.001 PHE D 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 100 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.624 Fit side-chains REVERT: A 13 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: A 61 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: A 228 ASP cc_start: 0.8367 (m-30) cc_final: 0.8105 (m-30) REVERT: D 13 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: D 228 ASP cc_start: 0.8395 (m-30) cc_final: 0.8128 (m-30) REVERT: D 243 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7650 (tmm160) REVERT: E 13 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: E 56 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: E 61 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: E 228 ASP cc_start: 0.8427 (m-30) cc_final: 0.8161 (m-30) REVERT: E 260 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7237 (ttpp) outliers start: 32 outliers final: 13 residues processed: 94 average time/residue: 1.1264 time to fit residues: 111.8196 Evaluate side-chains 87 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.136508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115491 restraints weight = 6187.979| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.49 r_work: 0.3404 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4142 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= 0.173 Angle : 0.537 9.785 8826 Z= 0.261 Chirality : 0.038 0.114 954 Planarity : 0.005 0.043 1095 Dihedral : 8.149 83.422 887 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.46 % Favored : 96.15 % Rotamer: Outliers : 3.60 % Allowed : 21.44 % 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: 2.54 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.48 (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 A 224 PHE 0.010 0.001 PHE A 95 TYR 0.011 0.001 TYR D 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 90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.626 Fit side-chains REVERT: A 61 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: A 136 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7691 (mm) REVERT: A 203 LEU cc_start: 0.8325 (mp) cc_final: 0.8065 (mm) REVERT: A 228 ASP cc_start: 0.8172 (m-30) cc_final: 0.7910 (m-30) REVERT: D 136 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7603 (mm) REVERT: D 228 ASP cc_start: 0.8191 (m-30) cc_final: 0.7919 (m-30) REVERT: D 243 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7410 (tmm160) REVERT: E 56 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7003 (pm20) REVERT: E 61 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: E 136 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7608 (mm) REVERT: E 203 LEU cc_start: 0.8395 (mp) cc_final: 0.8133 (mm) REVERT: E 228 ASP cc_start: 0.8228 (m-30) cc_final: 0.7994 (m-30) outliers start: 23 outliers final: 9 residues processed: 85 average time/residue: 1.0589 time to fit residues: 95.4284 Evaluate side-chains 85 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 4.9990 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114088 restraints weight = 6274.081| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.50 r_work: 0.3373 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4137 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= 0.198 Angle : 0.557 10.473 8826 Z= 0.269 Chirality : 0.038 0.114 954 Planarity : 0.005 0.043 1095 Dihedral : 7.293 85.037 878 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.59 % Favored : 96.03 % Rotamer: Outliers : 4.23 % Allowed : 20.66 % 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: 3.02 (0.29), residues: 780 helix: 2.54 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.55 (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 D 224 PHE 0.013 0.001 PHE A 95 TYR 0.011 0.001 TYR D 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 102 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.653 Fit side-chains REVERT: A 13 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: A 61 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: A 136 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7917 (mm) REVERT: A 203 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8317 (mm) REVERT: A 228 ASP cc_start: 0.8347 (m-30) cc_final: 0.8090 (m-30) REVERT: D 13 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: D 136 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7863 (mm) REVERT: D 228 ASP cc_start: 0.8374 (m-30) cc_final: 0.8126 (m-30) REVERT: D 243 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7605 (tmm160) REVERT: E 13 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: E 56 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: E 61 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8025 (pm20) REVERT: E 136 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7846 (mm) REVERT: E 203 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8339 (mm) REVERT: E 228 ASP cc_start: 0.8413 (m-30) cc_final: 0.8160 (m-30) outliers start: 27 outliers final: 8 residues processed: 93 average time/residue: 1.0122 time to fit residues: 99.8348 Evaluate side-chains 94 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 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 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 Chi-restraints excluded: chain E residue 203 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 121 ASN D 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115156 restraints weight = 6288.575| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.46 r_work: 0.3366 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4167 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= 0.192 Angle : 0.552 10.178 8826 Z= 0.267 Chirality : 0.038 0.115 954 Planarity : 0.005 0.043 1095 Dihedral : 7.264 84.763 878 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.97 % Favored : 95.64 % Rotamer: Outliers : 2.97 % Allowed : 21.60 % Favored : 75.43 % 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: 3.05 (0.29), residues: 780 helix: 2.55 (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 0.010 0.001 TRP A 184 HIS 0.003 0.001 HIS E 224 PHE 0.014 0.001 PHE A 95 TYR 0.011 0.001 TYR D 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 90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.706 Fit side-chains REVERT: A 13 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: A 136 LEU cc_start: 0.8080 (mt) cc_final: 0.7854 (mm) REVERT: A 203 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8234 (mm) REVERT: A 228 ASP cc_start: 0.8301 (m-30) cc_final: 0.8041 (m-30) REVERT: D 13 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: D 136 LEU cc_start: 0.8031 (mt) cc_final: 0.7791 (mm) REVERT: D 203 LEU cc_start: 0.8494 (mp) cc_final: 0.8247 (mm) REVERT: D 228 ASP cc_start: 0.8328 (m-30) cc_final: 0.8080 (m-30) REVERT: D 243 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7542 (tmm160) REVERT: E 13 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: E 61 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: E 136 LEU cc_start: 0.8025 (mt) cc_final: 0.7771 (mm) REVERT: E 203 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8273 (mm) REVERT: E 228 ASP cc_start: 0.8368 (m-30) cc_final: 0.8108 (m-30) outliers start: 19 outliers final: 8 residues processed: 84 average time/residue: 1.0589 time to fit residues: 94.4304 Evaluate side-chains 85 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain E residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN D 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116354 restraints weight = 6303.628| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.50 r_work: 0.3292 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6465 Z= 0.162 Angle : 0.530 9.155 8826 Z= 0.258 Chirality : 0.038 0.114 954 Planarity : 0.005 0.044 1095 Dihedral : 6.929 82.662 875 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.46 % Favored : 96.15 % Rotamer: Outliers : 2.19 % Allowed : 22.38 % Favored : 75.43 % 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: 3.16 (0.29), residues: 780 helix: 2.64 (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 0.009 0.001 TRP A 184 HIS 0.002 0.001 HIS D 224 PHE 0.015 0.001 PHE A 95 TYR 0.011 0.001 TYR D 86 ARG 0.001 0.000 ARG A 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 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.628 Fit side-chains REVERT: A 13 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: A 203 LEU cc_start: 0.8392 (mp) cc_final: 0.8169 (mm) REVERT: A 228 ASP cc_start: 0.8107 (m-30) cc_final: 0.7856 (m-30) REVERT: D 13 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: D 200 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7208 (t80) REVERT: D 203 LEU cc_start: 0.8395 (mp) cc_final: 0.8159 (mm) REVERT: D 228 ASP cc_start: 0.8117 (m-30) cc_final: 0.7860 (m-30) REVERT: E 13 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: E 61 GLU cc_start: 0.8046 (mp0) cc_final: 0.7817 (pm20) REVERT: E 203 LEU cc_start: 0.8441 (mp) cc_final: 0.8219 (mm) REVERT: E 228 ASP cc_start: 0.8165 (m-30) cc_final: 0.7933 (m-30) outliers start: 14 outliers final: 8 residues processed: 77 average time/residue: 0.9375 time to fit residues: 77.0941 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 : 0.767 ------------------------------------------------------------------------------- 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 200 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: 2.9990 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111739 restraints weight = 6399.225| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.47 r_work: 0.3343 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6465 Z= 0.254 Angle : 0.562 5.904 8826 Z= 0.281 Chirality : 0.040 0.114 954 Planarity : 0.005 0.044 1095 Dihedral : 7.155 87.634 872 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.82 % Favored : 96.79 % Rotamer: Outliers : 2.50 % Allowed : 22.38 % 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: 2.84 (0.29), residues: 780 helix: 2.44 (0.20), residues: 564 sheet: None (None), residues: 0 loop : 0.43 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 184 HIS 0.005 0.001 HIS E 224 PHE 0.017 0.002 PHE A 95 TYR 0.011 0.001 TYR D 76 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: 5431.42 seconds wall clock time: 99 minutes 11.54 seconds (5951.54 seconds total)