Starting phenix.real_space_refine on Tue Aug 4 19:10:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgj_44514/08_2026/9bgj_44514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgj_44514/08_2026/9bgj_44514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bgj_44514/08_2026/9bgj_44514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgj_44514/08_2026/9bgj_44514.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgj_44514/08_2026/9bgj_44514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgj_44514/08_2026/9bgj_44514.cif" } resolution = 3.34 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= 0.005 sd= 0.069 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: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 2 5.21 5 S 18 5.16 5 C 3849 2.51 5 N 1145 2.21 5 O 1297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6361 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2669 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 517 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "B" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2640 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 19, 'TRANS': 314} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 524 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 1.13, per 1000 atoms: 0.18 Number of scatterers: 6361 At special positions: 0 Unit cell: (82.17, 83.83, 100.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 50 15.00 Mg 2 11.99 O 1297 8.00 N 1145 7.00 C 3849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 212.1 milliseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1258 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 4 sheets defined 51.0% alpha, 6.0% beta 19 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.643A pdb=" N ARG A 18 " --> pdb=" O THR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.528A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 90 through 123 removed outlier: 3.912A pdb=" N LYS A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 143 Processing helix chain 'A' and resid 161 through 177 removed outlier: 4.595A pdb=" N VAL A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.556A pdb=" N ARG A 205 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 206 " --> pdb=" O MET A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 206' Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 222 through 227 removed outlier: 3.835A pdb=" N ARG A 225 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.982A pdb=" N ILE A 235 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.680A pdb=" N LEU A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.854A pdb=" N LEU A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.744A pdb=" N ARG B 18 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.526A pdb=" N GLY B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 90 through 123 removed outlier: 3.941A pdb=" N LYS B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 143 Processing helix chain 'B' and resid 161 through 177 removed outlier: 5.264A pdb=" N VAL B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.259A pdb=" N ARG B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 250 through 265 removed outlier: 3.726A pdb=" N LEU B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 318 through 335 removed outlier: 3.891A pdb=" N LEU B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 148 removed outlier: 6.316A pdb=" N ALA A 238 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N HIS A 278 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA A 240 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TYR A 314 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 277 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 148 removed outlier: 6.777A pdb=" N VAL B 193 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 235 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLU B 276 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA B 238 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS B 278 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 240 " --> pdb=" O HIS B 278 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N TYR B 314 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 0.73 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1687 1.33 - 1.45: 1379 1.45 - 1.57: 3395 1.57 - 1.69: 99 1.69 - 1.80: 32 Bond restraints: 6592 Sorted by residual: bond pdb=" C5' DG C 25 " pdb=" C4' DG C 25 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.14e+01 bond pdb=" C3' DA D 3 " pdb=" C2' DA D 3 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.11e+00 bond pdb=" C3' DA D 11 " pdb=" C2' DA D 11 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.99e+00 bond pdb=" C3' DA C 11 " pdb=" C2' DA C 11 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.12e+00 bond pdb=" C3' DT C 24 " pdb=" C2' DT C 24 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.49e+00 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 8568 1.10 - 2.20: 449 2.20 - 3.29: 111 3.29 - 4.39: 20 4.39 - 5.49: 12 Bond angle restraints: 9160 Sorted by residual: angle pdb=" O5' DG C 25 " pdb=" C5' DG C 25 " pdb=" C4' DG C 25 " ideal model delta sigma weight residual 109.40 112.84 -3.44 8.00e-01 1.56e+00 1.85e+01 angle pdb=" N3 DT C 7 " pdb=" C4 DT C 7 " pdb=" O4 DT C 7 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" O4' DG C 23 " pdb=" C4' DG C 23 " pdb=" C3' DG C 23 " ideal model delta sigma weight residual 106.00 103.49 2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT C 6 " pdb=" C4 DT C 6 " pdb=" O4 DT C 6 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT C 24 " pdb=" C4 DT C 24 " pdb=" O4 DT C 24 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 9155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.21: 3028 19.21 - 38.41: 474 38.41 - 57.62: 273 57.62 - 76.82: 32 76.82 - 96.03: 11 Dihedral angle restraints: 3818 sinusoidal: 1871 harmonic: 1947 Sorted by residual: dihedral pdb=" CA GLN B 129 " pdb=" C GLN B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA GLN A 129 " pdb=" C GLN A 129 " pdb=" N PRO A 130 " pdb=" CA PRO A 130 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CG ARG B 308 " pdb=" CD ARG B 308 " pdb=" NE ARG B 308 " pdb=" CZ ARG B 308 " ideal model delta sinusoidal sigma weight residual -180.00 -135.52 -44.48 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 3815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 615 0.033 - 0.066: 271 0.066 - 0.099: 76 0.099 - 0.131: 42 0.131 - 0.164: 4 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CA TYR A 297 " pdb=" N TYR A 297 " pdb=" C TYR A 297 " pdb=" CB TYR A 297 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA VAL B 161 " pdb=" N VAL B 161 " pdb=" C VAL B 161 " pdb=" CB VAL B 161 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" C3' DT D 16 " pdb=" C4' DT D 16 " pdb=" O3' DT D 16 " pdb=" C2' DT D 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1005 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 85 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" CG ASP A 85 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 85 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 85 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 231 " 0.024 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO B 232 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 232 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 232 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 231 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO A 232 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.019 5.00e-02 4.00e+02 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 55 2.52 - 3.11: 4509 3.11 - 3.71: 10089 3.71 - 4.30: 14248 4.30 - 4.90: 23596 Nonbonded interactions: 52497 Sorted by model distance: nonbonded pdb=" OP1 DC D 12 " pdb="MG MG B 401 " model vdw 1.922 2.170 nonbonded pdb=" OP1 DC C 12 " pdb="MG MG A 401 " model vdw 1.925 2.170 nonbonded pdb=" O PHE B 241 " pdb="MG MG B 401 " model vdw 2.117 2.170 nonbonded pdb=" O PHE A 241 " pdb="MG MG A 401 " model vdw 2.182 2.170 nonbonded pdb=" OD2 ASP B 188 " pdb="MG MG B 401 " model vdw 2.216 2.170 ... (remaining 52492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 299 or resid 304 through 401)) selection = chain 'B' } 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: 2.780 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.460 Find NCS groups from input model: 0.050 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6592 Z= 0.310 Angle : 0.610 5.488 9160 Z= 0.437 Chirality : 0.044 0.164 1008 Planarity : 0.004 0.037 1028 Dihedral : 22.775 96.030 2560 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.93 % Allowed : 26.43 % Favored : 69.64 % 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: -0.13 (0.35), residues: 666 helix: 0.95 (0.33), residues: 282 sheet: -1.23 (0.73), residues: 43 loop : -0.78 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 225 TYR 0.017 0.001 TYR A 297 PHE 0.021 0.001 PHE B 171 TRP 0.011 0.001 TRP A 117 HIS 0.001 0.000 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.31 ( 6592) covalent geometry : angle 0.60985 / 0.44 ( 9160) hydrogen bonds : bond 0.15872 / 10.46 ( 264) hydrogen bonds : angle 5.41762 / 3.77 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.129 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: A 24 ARG cc_start: 0.6699 (tmt170) cc_final: 0.5822 (tpt-90) REVERT: A 103 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8099 (tt0) REVERT: A 196 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8514 (mm-30) REVERT: B 24 ARG cc_start: 0.6069 (tmt170) cc_final: 0.2271 (mtm180) REVERT: B 85 ASP cc_start: 0.7848 (t0) cc_final: 0.7435 (t0) REVERT: B 142 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7780 (mtp-110) REVERT: B 166 GLU cc_start: 0.7609 (tp30) cc_final: 0.7327 (mt-10) REVERT: B 202 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6892 (mp0) outliers start: 22 outliers final: 18 residues processed: 76 average time/residue: 0.0771 time to fit residues: 7.5962 Evaluate side-chains 80 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 40.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN B 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.162655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118202 restraints weight = 6591.678| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.94 r_work: 0.3178 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6592 Z= 0.180 Angle : 0.570 5.686 9160 Z= 0.304 Chirality : 0.043 0.169 1008 Planarity : 0.004 0.036 1028 Dihedral : 23.688 97.130 1325 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.71 % Allowed : 24.46 % Favored : 69.82 % 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: 0.37 (0.35), residues: 666 helix: 1.54 (0.33), residues: 267 sheet: -1.47 (0.72), residues: 44 loop : -0.50 (0.37), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.005 0.001 PHE B 87 TRP 0.012 0.002 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 6592) covalent geometry : angle 0.57046 / 0.30 ( 9160) hydrogen bonds : bond 0.04713 / 3.18 ( 264) hydrogen bonds : angle 3.98528 / 2.82 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.137 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: A 24 ARG cc_start: 0.6556 (tmt170) cc_final: 0.5707 (tpt-90) REVERT: A 85 ASP cc_start: 0.7443 (t0) cc_final: 0.7215 (t0) REVERT: A 103 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8163 (tt0) REVERT: A 124 GLU cc_start: 0.8346 (mp0) cc_final: 0.8142 (mp0) REVERT: A 196 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8576 (mm-30) REVERT: B 24 ARG cc_start: 0.6121 (tmt170) cc_final: 0.2275 (mtm180) REVERT: B 85 ASP cc_start: 0.7879 (t0) cc_final: 0.7562 (t0) REVERT: B 142 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7749 (mtp-110) REVERT: B 166 GLU cc_start: 0.7581 (tp30) cc_final: 0.7305 (mt-10) REVERT: B 202 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6962 (mp0) outliers start: 32 outliers final: 19 residues processed: 92 average time/residue: 0.0666 time to fit residues: 8.1907 Evaluate side-chains 86 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 289 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 50.0000 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.163305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118466 restraints weight = 6548.217| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.96 r_work: 0.3192 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6592 Z= 0.151 Angle : 0.540 5.462 9160 Z= 0.288 Chirality : 0.042 0.168 1008 Planarity : 0.004 0.035 1028 Dihedral : 23.651 96.639 1312 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 6.07 % Allowed : 24.29 % Favored : 69.64 % 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: 0.46 (0.35), residues: 666 helix: 1.67 (0.33), residues: 267 sheet: -1.44 (0.76), residues: 41 loop : -0.52 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.005 0.001 PHE A 288 TRP 0.012 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 6592) covalent geometry : angle 0.54014 / 0.29 ( 9160) hydrogen bonds : bond 0.04231 / 2.85 ( 264) hydrogen bonds : angle 3.81602 / 2.69 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 0.206 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6493 (tmt170) cc_final: 0.5673 (tpt-90) REVERT: A 86 ASP cc_start: 0.8172 (t0) cc_final: 0.7807 (t0) REVERT: A 103 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8101 (tt0) REVERT: A 124 GLU cc_start: 0.8337 (mp0) cc_final: 0.8083 (mp0) REVERT: A 196 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8528 (mm-30) REVERT: B 24 ARG cc_start: 0.6065 (tmt170) cc_final: 0.2185 (mtm180) REVERT: B 85 ASP cc_start: 0.7876 (t0) cc_final: 0.7540 (t0) REVERT: B 166 GLU cc_start: 0.7548 (tp30) cc_final: 0.7167 (mt-10) REVERT: B 202 GLU cc_start: 0.7667 (mt-10) cc_final: 0.6956 (mp0) REVERT: B 264 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7313 (mp) outliers start: 34 outliers final: 20 residues processed: 96 average time/residue: 0.0581 time to fit residues: 7.5614 Evaluate side-chains 86 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 289 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.0670 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.166895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122016 restraints weight = 6551.332| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.97 r_work: 0.3234 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6592 Z= 0.112 Angle : 0.511 5.769 9160 Z= 0.274 Chirality : 0.041 0.165 1008 Planarity : 0.003 0.033 1028 Dihedral : 23.405 95.280 1309 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.00 % Allowed : 23.93 % Favored : 71.07 % 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: 0.65 (0.35), residues: 666 helix: 1.90 (0.33), residues: 267 sheet: -1.41 (0.76), residues: 41 loop : -0.46 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.006 0.001 PHE B 87 TRP 0.010 0.001 TRP A 117 HIS 0.001 0.000 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 6592) covalent geometry : angle 0.51102 / 0.27 ( 9160) hydrogen bonds : bond 0.03609 / 2.42 ( 264) hydrogen bonds : angle 3.58910 / 2.55 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.123 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: A 24 ARG cc_start: 0.6395 (tmt170) cc_final: 0.5523 (tpt-90) REVERT: A 103 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8015 (tt0) REVERT: A 124 GLU cc_start: 0.8235 (mp0) cc_final: 0.7971 (mp0) REVERT: A 196 GLU cc_start: 0.8859 (tt0) cc_final: 0.8518 (mm-30) REVERT: B 24 ARG cc_start: 0.5917 (tmt170) cc_final: 0.2060 (mtm180) REVERT: B 85 ASP cc_start: 0.7805 (t0) cc_final: 0.7434 (t0) REVERT: B 166 GLU cc_start: 0.7528 (tp30) cc_final: 0.7147 (mt-10) REVERT: B 202 GLU cc_start: 0.7596 (mt-10) cc_final: 0.6851 (mp0) REVERT: B 264 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7239 (mp) REVERT: B 312 GLU cc_start: 0.8813 (tt0) cc_final: 0.8255 (tt0) outliers start: 28 outliers final: 17 residues processed: 89 average time/residue: 0.0681 time to fit residues: 7.9205 Evaluate side-chains 82 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 289 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 0.0040 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.166481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121457 restraints weight = 6656.924| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.98 r_work: 0.3225 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6592 Z= 0.122 Angle : 0.508 5.680 9160 Z= 0.271 Chirality : 0.041 0.167 1008 Planarity : 0.003 0.032 1028 Dihedral : 23.392 94.857 1305 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.82 % Allowed : 23.75 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.35), residues: 666 helix: 1.92 (0.33), residues: 267 sheet: -1.31 (0.77), residues: 41 loop : -0.43 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.005 0.001 PHE B 87 TRP 0.010 0.001 TRP A 117 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6592) covalent geometry : angle 0.50810 / 0.27 ( 9160) hydrogen bonds : bond 0.03538 / 2.38 ( 264) hydrogen bonds : angle 3.57329 / 2.52 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.206 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: A 24 ARG cc_start: 0.6399 (tmt170) cc_final: 0.5551 (tpt-90) REVERT: A 103 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8034 (tt0) REVERT: A 124 GLU cc_start: 0.8182 (mp0) cc_final: 0.7899 (mp0) REVERT: A 196 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8547 (mm-30) REVERT: B 24 ARG cc_start: 0.5897 (tmt170) cc_final: 0.2068 (mtm180) REVERT: B 85 ASP cc_start: 0.7797 (t0) cc_final: 0.7441 (t0) REVERT: B 202 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6864 (mp0) REVERT: B 264 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7203 (mp) outliers start: 27 outliers final: 21 residues processed: 86 average time/residue: 0.0688 time to fit residues: 7.9488 Evaluate side-chains 86 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 264 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.166365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121269 restraints weight = 6602.633| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.98 r_work: 0.3225 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6592 Z= 0.123 Angle : 0.505 5.709 9160 Z= 0.269 Chirality : 0.041 0.168 1008 Planarity : 0.004 0.031 1028 Dihedral : 23.402 94.314 1305 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.36 % Allowed : 23.39 % Favored : 71.25 % 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: 0.75 (0.35), residues: 666 helix: 1.96 (0.33), residues: 267 sheet: -1.21 (0.78), residues: 41 loop : -0.41 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 29 TYR 0.017 0.001 TYR A 297 PHE 0.004 0.001 PHE B 87 TRP 0.009 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6592) covalent geometry : angle 0.50532 / 0.27 ( 9160) hydrogen bonds : bond 0.03449 / 2.32 ( 264) hydrogen bonds : angle 3.52485 / 2.49 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.157 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: A 24 ARG cc_start: 0.6403 (tmt170) cc_final: 0.5566 (tpt-90) REVERT: A 103 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8063 (tt0) REVERT: A 124 GLU cc_start: 0.8166 (mp0) cc_final: 0.7879 (mp0) REVERT: A 196 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8548 (mm-30) REVERT: B 24 ARG cc_start: 0.5946 (tmt170) cc_final: 0.2102 (mtm180) REVERT: B 85 ASP cc_start: 0.7806 (t0) cc_final: 0.7485 (t0) REVERT: B 142 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7937 (mtm180) REVERT: B 166 GLU cc_start: 0.7526 (tp30) cc_final: 0.7145 (mt-10) REVERT: B 202 GLU cc_start: 0.7714 (mt-10) cc_final: 0.6987 (tp30) REVERT: B 225 ARG cc_start: 0.8556 (mtt90) cc_final: 0.8245 (mtt90) REVERT: B 260 MET cc_start: 0.8484 (ttt) cc_final: 0.8196 (ttt) REVERT: B 312 GLU cc_start: 0.8639 (tt0) cc_final: 0.8278 (tt0) outliers start: 30 outliers final: 23 residues processed: 91 average time/residue: 0.0637 time to fit residues: 7.6501 Evaluate side-chains 89 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 50.0000 chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 0.4980 chunk 46 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.159317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114359 restraints weight = 6668.971| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.93 r_work: 0.3130 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 6592 Z= 0.279 Angle : 0.624 5.598 9160 Z= 0.323 Chirality : 0.046 0.170 1008 Planarity : 0.005 0.048 1028 Dihedral : 23.886 95.571 1305 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 6.07 % Allowed : 22.68 % Favored : 71.25 % 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: 0.40 (0.35), residues: 666 helix: 1.57 (0.33), residues: 267 sheet: -1.47 (0.75), residues: 44 loop : -0.49 (0.37), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 29 TYR 0.017 0.002 TYR A 297 PHE 0.010 0.002 PHE B 102 TRP 0.012 0.002 TRP B 111 HIS 0.002 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.28 ( 6592) covalent geometry : angle 0.62358 / 0.32 ( 9160) hydrogen bonds : bond 0.04672 / 3.14 ( 264) hydrogen bonds : angle 3.84566 / 2.72 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.129 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: A 24 ARG cc_start: 0.6489 (tmt170) cc_final: 0.4936 (tpt90) REVERT: A 103 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8099 (tt0) REVERT: A 124 GLU cc_start: 0.8180 (mp0) cc_final: 0.7827 (mp0) REVERT: A 196 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8611 (mm-30) REVERT: B 24 ARG cc_start: 0.6095 (tmt170) cc_final: 0.2122 (mtm180) REVERT: B 85 ASP cc_start: 0.7932 (t0) cc_final: 0.7720 (t0) REVERT: B 142 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7980 (mtm180) REVERT: B 166 GLU cc_start: 0.7573 (tp30) cc_final: 0.7156 (mt-10) REVERT: B 180 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7835 (mp) REVERT: B 225 ARG cc_start: 0.8628 (mtt90) cc_final: 0.8355 (mpt-90) REVERT: B 260 MET cc_start: 0.8502 (ttt) cc_final: 0.8275 (ttt) outliers start: 34 outliers final: 22 residues processed: 89 average time/residue: 0.0628 time to fit residues: 7.5429 Evaluate side-chains 89 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.164642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119980 restraints weight = 6523.717| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.95 r_work: 0.3207 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6592 Z= 0.114 Angle : 0.523 5.829 9160 Z= 0.277 Chirality : 0.041 0.167 1008 Planarity : 0.004 0.032 1028 Dihedral : 23.593 94.226 1305 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.46 % Allowed : 23.57 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.35), residues: 666 helix: 1.88 (0.33), residues: 267 sheet: -1.20 (0.75), residues: 46 loop : -0.44 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.018 0.001 TYR A 297 PHE 0.006 0.001 PHE B 87 TRP 0.010 0.001 TRP B 156 HIS 0.002 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6592) covalent geometry : angle 0.52254 / 0.28 ( 9160) hydrogen bonds : bond 0.03641 / 2.48 ( 264) hydrogen bonds : angle 3.57885 / 2.53 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.150 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: A 24 ARG cc_start: 0.6443 (tmt170) cc_final: 0.5596 (tpt-90) REVERT: A 103 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8036 (tt0) REVERT: A 124 GLU cc_start: 0.8145 (mp0) cc_final: 0.7785 (mp0) REVERT: A 163 GLU cc_start: 0.8448 (mp0) cc_final: 0.8213 (mp0) REVERT: A 196 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8570 (mm-30) REVERT: B 17 GLU cc_start: 0.8048 (tt0) cc_final: 0.7740 (mt-10) REVERT: B 24 ARG cc_start: 0.5935 (tmt170) cc_final: 0.2052 (mtm180) REVERT: B 85 ASP cc_start: 0.7812 (t0) cc_final: 0.7567 (t0) REVERT: B 142 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7960 (mtm180) REVERT: B 166 GLU cc_start: 0.7553 (tp30) cc_final: 0.7151 (mt-10) REVERT: B 180 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7757 (mp) REVERT: B 202 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7052 (tp30) REVERT: B 312 GLU cc_start: 0.8672 (tt0) cc_final: 0.8379 (tt0) outliers start: 25 outliers final: 17 residues processed: 85 average time/residue: 0.0686 time to fit residues: 7.6437 Evaluate side-chains 88 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 40 optimal weight: 0.2980 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 41 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.164034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119170 restraints weight = 6684.807| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.96 r_work: 0.3197 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6592 Z= 0.136 Angle : 0.520 5.745 9160 Z= 0.274 Chirality : 0.042 0.170 1008 Planarity : 0.004 0.031 1028 Dihedral : 23.535 93.884 1305 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.93 % Allowed : 24.46 % Favored : 71.61 % 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: 0.57 (0.35), residues: 666 helix: 1.74 (0.33), residues: 273 sheet: -1.15 (0.76), residues: 46 loop : -0.49 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.018 0.001 TYR A 297 PHE 0.004 0.001 PHE B 54 TRP 0.011 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 6592) covalent geometry : angle 0.52007 / 0.27 ( 9160) hydrogen bonds : bond 0.03604 / 2.43 ( 264) hydrogen bonds : angle 3.56869 / 2.52 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.143 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: A 24 ARG cc_start: 0.6429 (tmt170) cc_final: 0.5640 (tpt-90) REVERT: A 103 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8021 (tt0) REVERT: A 124 GLU cc_start: 0.8147 (mp0) cc_final: 0.7789 (mp0) REVERT: A 163 GLU cc_start: 0.8441 (mp0) cc_final: 0.8211 (mp0) REVERT: A 196 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8549 (mm-30) REVERT: B 17 GLU cc_start: 0.8049 (tt0) cc_final: 0.7737 (mt-10) REVERT: B 24 ARG cc_start: 0.6016 (tmt170) cc_final: 0.2153 (mtm180) REVERT: B 85 ASP cc_start: 0.7831 (t0) cc_final: 0.7628 (t0) REVERT: B 142 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7962 (mtm180) REVERT: B 166 GLU cc_start: 0.7557 (tp30) cc_final: 0.7188 (mt-10) REVERT: B 180 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7782 (mp) REVERT: B 202 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7040 (tp30) REVERT: B 312 GLU cc_start: 0.8682 (tt0) cc_final: 0.8411 (tt0) outliers start: 22 outliers final: 16 residues processed: 85 average time/residue: 0.0657 time to fit residues: 7.3267 Evaluate side-chains 87 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 chunk 34 optimal weight: 10.0000 chunk 68 optimal weight: 50.0000 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.167168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122776 restraints weight = 6563.633| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.93 r_work: 0.3240 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6592 Z= 0.108 Angle : 0.505 6.253 9160 Z= 0.268 Chirality : 0.041 0.168 1008 Planarity : 0.003 0.031 1028 Dihedral : 23.316 93.535 1305 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.39 % Allowed : 25.36 % Favored : 71.25 % 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: 0.65 (0.35), residues: 666 helix: 1.86 (0.33), residues: 273 sheet: -1.08 (0.77), residues: 46 loop : -0.49 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.006 0.001 PHE B 87 TRP 0.012 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 6592) covalent geometry : angle 0.50504 / 0.27 ( 9160) hydrogen bonds : bond 0.03225 / 2.16 ( 264) hydrogen bonds : angle 3.46318 / 2.44 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.124 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7361 (tm-30) REVERT: A 24 ARG cc_start: 0.6353 (tmt170) cc_final: 0.5381 (tpt-90) REVERT: A 103 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8035 (tt0) REVERT: A 124 GLU cc_start: 0.8110 (mp0) cc_final: 0.7836 (mp0) REVERT: A 196 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8555 (mm-30) REVERT: B 17 GLU cc_start: 0.8053 (tt0) cc_final: 0.7753 (mt-10) REVERT: B 24 ARG cc_start: 0.5864 (tmt170) cc_final: 0.2041 (mtm180) REVERT: B 85 ASP cc_start: 0.7753 (t0) cc_final: 0.7525 (t0) REVERT: B 142 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7960 (mtm180) REVERT: B 166 GLU cc_start: 0.7561 (tp30) cc_final: 0.7150 (mt-10) REVERT: B 180 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7766 (mp) REVERT: B 202 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7035 (tp30) REVERT: B 225 ARG cc_start: 0.8572 (mtt90) cc_final: 0.8289 (mtt90) REVERT: B 312 GLU cc_start: 0.8698 (tt0) cc_final: 0.8437 (tt0) outliers start: 19 outliers final: 14 residues processed: 78 average time/residue: 0.0736 time to fit residues: 7.4600 Evaluate side-chains 82 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.161185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116856 restraints weight = 6666.101| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.91 r_work: 0.3160 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6592 Z= 0.218 Angle : 0.570 5.676 9160 Z= 0.296 Chirality : 0.044 0.171 1008 Planarity : 0.004 0.037 1028 Dihedral : 23.626 94.552 1304 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.64 % Allowed : 24.29 % Favored : 71.07 % 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: 0.48 (0.35), residues: 666 helix: 1.61 (0.33), residues: 273 sheet: -1.17 (0.78), residues: 46 loop : -0.49 (0.38), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 29 TYR 0.017 0.002 TYR A 297 PHE 0.007 0.001 PHE B 102 TRP 0.012 0.002 TRP B 156 HIS 0.001 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 ( 6592) covalent geometry : angle 0.56998 / 0.30 ( 9160) hydrogen bonds : bond 0.04096 / 2.74 ( 264) hydrogen bonds : angle 3.68121 / 2.60 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1346.78 seconds wall clock time: 23 minutes 39.31 seconds (1419.31 seconds total)