Starting phenix.real_space_refine on Wed Jun 3 13:45:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wq2_66157/06_2026/9wq2_66157.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wq2_66157/06_2026/9wq2_66157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wq2_66157/06_2026/9wq2_66157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wq2_66157/06_2026/9wq2_66157.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wq2_66157/06_2026/9wq2_66157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wq2_66157/06_2026/9wq2_66157.map" } resolution = 3.27 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= 0.001 sd= 0.065 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 P 4 5.49 5 S 6 5.16 5 C 3870 2.51 5 N 1002 2.21 5 O 1122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6004 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2957 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 9, 'TRANS': 358} Chain: "A" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2957 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 9, 'TRANS': 358} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.86, per 1000 atoms: 0.31 Number of scatterers: 6004 At special positions: 0 Unit cell: (65.57, 107.07, 111.22, 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) S 6 16.00 P 4 15.00 O 1122 8.00 N 1002 7.00 C 3870 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: 0.51 Conformation dependent library (CDL) restraints added in 379.0 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 4 sheets defined 51.0% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 29 through 49 removed outlier: 3.958A pdb=" N PHE B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 69 Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 83 through 105 Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.666A pdb=" N ASN B 123 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 154 through 177 removed outlier: 3.760A pdb=" N VAL B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 189 through 199 Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.843A pdb=" N SER B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 309 removed outlier: 3.677A pdb=" N ASN B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 333 Processing helix chain 'A' and resid 3 through 24 Processing helix chain 'A' and resid 29 through 49 removed outlier: 3.978A pdb=" N PHE A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 69 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 83 through 105 Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.666A pdb=" N ASN A 123 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 142 through 152 Processing helix chain 'A' and resid 154 through 177 removed outlier: 3.759A pdb=" N VAL A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 189 through 199 Processing helix chain 'A' and resid 238 through 243 removed outlier: 3.843A pdb=" N SER A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 removed outlier: 3.678A pdb=" N ASN A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing sheet with id=AA1, first strand: chain 'B' and resid 135 through 141 removed outlier: 6.661A pdb=" N TYR B 109 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR B 185 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU B 111 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE B 187 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 113 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG B 182 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TYR B 209 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TYR B 184 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ARG B 211 " --> pdb=" O TYR B 184 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N GLY B 186 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP B 217 " --> pdb=" O ASN B 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 233 removed outlier: 3.635A pdb=" N LYS B 276 " --> pdb=" O THR B 232 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 344 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE B 319 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE B 346 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TRP B 353 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 141 removed outlier: 6.661A pdb=" N TYR A 109 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR A 185 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU A 111 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE A 187 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 113 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A 182 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TYR A 209 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TYR A 184 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ARG A 211 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N GLY A 186 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 217 " --> pdb=" O ASN A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 removed outlier: 3.635A pdb=" N LYS A 276 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 344 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE A 319 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE A 346 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP A 353 " --> pdb=" O HIS A 345 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.95 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 972 1.31 - 1.43: 1556 1.43 - 1.55: 3586 1.55 - 1.68: 8 1.68 - 1.80: 10 Bond restraints: 6132 Sorted by residual: bond pdb=" C36 1SY B 401 " pdb=" N42 1SY B 401 " ideal model delta sigma weight residual 1.357 1.494 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C36 1SY A 401 " pdb=" N42 1SY A 401 " ideal model delta sigma weight residual 1.357 1.493 -0.136 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C40 1SY B 401 " pdb=" N39 1SY B 401 " ideal model delta sigma weight residual 1.304 1.436 -0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C40 1SY A 401 " pdb=" N39 1SY A 401 " ideal model delta sigma weight residual 1.304 1.436 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C6 1SY A 401 " pdb=" N01 1SY A 401 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.00e-02 2.50e+03 3.55e+01 ... (remaining 6127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 8252 3.76 - 7.53: 42 7.53 - 11.29: 14 11.29 - 15.05: 10 15.05 - 18.82: 4 Bond angle restraints: 8322 Sorted by residual: angle pdb=" O19 1SY B 401 " pdb=" P18 1SY B 401 " pdb=" O44 1SY B 401 " ideal model delta sigma weight residual 123.21 104.39 18.82 3.00e+00 1.11e-01 3.93e+01 angle pdb=" O19 1SY A 401 " pdb=" P18 1SY A 401 " pdb=" O44 1SY A 401 " ideal model delta sigma weight residual 123.21 104.40 18.81 3.00e+00 1.11e-01 3.93e+01 angle pdb=" O29 1SY B 401 " pdb=" P27 1SY B 401 " pdb=" O30 1SY B 401 " ideal model delta sigma weight residual 123.47 106.48 16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" O29 1SY A 401 " pdb=" P27 1SY A 401 " pdb=" O30 1SY A 401 " ideal model delta sigma weight residual 123.47 106.48 16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" N01 1SY B 401 " pdb=" C6 1SY B 401 " pdb=" N1 1SY B 401 " ideal model delta sigma weight residual 119.32 105.96 13.36 3.00e+00 1.11e-01 1.98e+01 ... (remaining 8317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.23: 3401 26.23 - 52.46: 251 52.46 - 78.69: 56 78.69 - 104.92: 12 104.92 - 131.15: 10 Dihedral angle restraints: 3730 sinusoidal: 1580 harmonic: 2150 Sorted by residual: dihedral pdb=" C3' 1SY A 401 " pdb=" O28 1SY A 401 " pdb=" P27 1SY A 401 " pdb=" O30 1SY A 401 " ideal model delta sinusoidal sigma weight residual -150.53 -19.38 -131.15 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C3' 1SY B 401 " pdb=" O28 1SY B 401 " pdb=" P27 1SY B 401 " pdb=" O30 1SY B 401 " ideal model delta sinusoidal sigma weight residual -150.53 -19.42 -131.11 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C25 1SY B 401 " pdb=" O26 1SY B 401 " pdb=" P27 1SY B 401 " pdb=" O29 1SY B 401 " ideal model delta sinusoidal sigma weight residual 209.61 84.84 124.77 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 3727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 631 0.036 - 0.072: 249 0.072 - 0.108: 52 0.108 - 0.144: 32 0.144 - 0.179: 6 Chirality restraints: 970 Sorted by residual: chirality pdb=" C24 1SY B 401 " pdb=" C22 1SY B 401 " pdb=" C25 1SY B 401 " pdb=" O31 1SY B 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.61 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" C24 1SY A 401 " pdb=" C22 1SY A 401 " pdb=" C25 1SY A 401 " pdb=" O31 1SY A 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.61 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" C2' 1SY B 401 " pdb=" C1' 1SY B 401 " pdb=" C3' 1SY B 401 " pdb=" O2' 1SY B 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.58 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 967 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 270 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 271 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 270 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 271 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 271 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 271 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 325 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO B 326 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 326 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 326 " -0.020 5.00e-02 4.00e+02 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1398 2.79 - 3.32: 5497 3.32 - 3.85: 9526 3.85 - 4.37: 10911 4.37 - 4.90: 19524 Nonbonded interactions: 46856 Sorted by model distance: nonbonded pdb=" NH2 ARG B 120 " pdb=" OE2 GLU A 176 " model vdw 2.264 3.120 nonbonded pdb=" OE2 GLU B 176 " pdb=" NH2 ARG A 120 " model vdw 2.265 3.120 nonbonded pdb=" O SER A 177 " pdb=" OG SER A 177 " model vdw 2.278 3.040 nonbonded pdb=" O SER B 177 " pdb=" OG SER B 177 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR A 219 " pdb=" OD1 ASN A 283 " model vdw 2.281 3.040 ... (remaining 46851 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.690 Find NCS groups from input model: 0.040 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.008 0.137 6132 Z= 0.376 Angle : 0.941 18.817 8322 Z= 0.379 Chirality : 0.044 0.179 970 Planarity : 0.004 0.037 1032 Dihedral : 20.839 131.151 2342 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.15 % Allowed : 21.06 % Favored : 78.79 % 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: 0.47 (0.31), residues: 732 helix: 2.20 (0.28), residues: 328 sheet: -0.27 (0.43), residues: 138 loop : -1.87 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 303 TYR 0.010 0.001 TYR A 299 PHE 0.010 0.001 PHE B 228 TRP 0.002 0.001 TRP B 353 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.38 ( 6132) covalent geometry : angle 0.94088 / 0.38 ( 8322) hydrogen bonds : bond 0.14015 / 8.88 ( 315) hydrogen bonds : angle 5.13724 / 3.63 ( 921) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.258 Fit side-chains REVERT: B 303 ARG cc_start: 0.7899 (tpp80) cc_final: 0.7586 (tpp80) REVERT: A 303 ARG cc_start: 0.7905 (tpp80) cc_final: 0.7583 (tpp80) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1106 time to fit residues: 6.2522 Evaluate side-chains 38 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 2 ASN B 313 GLN A 2 ASN A 313 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117990 restraints weight = 7092.878| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.04 r_work: 0.3089 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6132 Z= 0.152 Angle : 0.546 5.687 8322 Z= 0.285 Chirality : 0.045 0.150 970 Planarity : 0.004 0.038 1032 Dihedral : 19.189 153.092 913 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.52 % Allowed : 18.18 % Favored : 80.30 % 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: 0.53 (0.32), residues: 732 helix: 2.30 (0.28), residues: 330 sheet: -0.28 (0.44), residues: 138 loop : -1.91 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 303 TYR 0.009 0.001 TYR B 299 PHE 0.010 0.001 PHE A 228 TRP 0.002 0.001 TRP A 353 HIS 0.002 0.001 HIS B 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 6132) covalent geometry : angle 0.54649 / 0.29 ( 8322) hydrogen bonds : bond 0.04639 / 2.94 ( 315) hydrogen bonds : angle 4.37033 / 3.05 ( 921) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.234 Fit side-chains REVERT: B 46 THR cc_start: 0.8785 (m) cc_final: 0.8490 (m) REVERT: B 303 ARG cc_start: 0.7926 (tpp80) cc_final: 0.7640 (tpp80) REVERT: A 303 ARG cc_start: 0.7925 (tpp80) cc_final: 0.7628 (tpp80) outliers start: 10 outliers final: 1 residues processed: 54 average time/residue: 0.0840 time to fit residues: 6.1529 Evaluate side-chains 44 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN A 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.164692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.117681 restraints weight = 7037.060| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.01 r_work: 0.3065 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6132 Z= 0.159 Angle : 0.534 5.476 8322 Z= 0.282 Chirality : 0.045 0.173 970 Planarity : 0.004 0.042 1032 Dihedral : 19.186 164.862 912 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.52 % Allowed : 18.33 % Favored : 80.15 % 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: 0.41 (0.32), residues: 732 helix: 2.34 (0.28), residues: 330 sheet: -0.45 (0.43), residues: 142 loop : -2.14 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 138 TYR 0.010 0.001 TYR B 219 PHE 0.010 0.001 PHE A 228 TRP 0.002 0.001 TRP B 353 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 6132) covalent geometry : angle 0.53432 / 0.28 ( 8322) hydrogen bonds : bond 0.04638 / 2.95 ( 315) hydrogen bonds : angle 4.33428 / 3.04 ( 921) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.226 Fit side-chains REVERT: B 46 THR cc_start: 0.8742 (m) cc_final: 0.8466 (m) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.0897 time to fit residues: 6.3899 Evaluate side-chains 50 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 302 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.0070 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN A 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.166826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119408 restraints weight = 7064.081| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.03 r_work: 0.3107 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6132 Z= 0.117 Angle : 0.492 5.016 8322 Z= 0.261 Chirality : 0.043 0.176 970 Planarity : 0.004 0.043 1032 Dihedral : 19.160 177.664 912 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.67 % Allowed : 18.18 % Favored : 80.15 % 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 (0.32), residues: 732 helix: 2.39 (0.28), residues: 330 sheet: -0.49 (0.43), residues: 142 loop : -2.22 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 303 TYR 0.010 0.001 TYR B 299 PHE 0.008 0.001 PHE B 146 TRP 0.001 0.001 TRP A 353 HIS 0.001 0.001 HIS B 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6132) covalent geometry : angle 0.49154 / 0.26 ( 8322) hydrogen bonds : bond 0.03925 / 2.50 ( 315) hydrogen bonds : angle 4.17866 / 2.94 ( 921) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.196 Fit side-chains REVERT: B 46 THR cc_start: 0.8665 (m) cc_final: 0.8382 (m) outliers start: 11 outliers final: 6 residues processed: 58 average time/residue: 0.0908 time to fit residues: 7.0545 Evaluate side-chains 50 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN A 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.163272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.115981 restraints weight = 7173.792| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.03 r_work: 0.3073 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6132 Z= 0.192 Angle : 0.571 6.321 8322 Z= 0.299 Chirality : 0.046 0.194 970 Planarity : 0.005 0.043 1032 Dihedral : 18.883 164.589 912 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.42 % Allowed : 18.18 % Favored : 79.39 % 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: 0.24 (0.31), residues: 732 helix: 2.27 (0.28), residues: 330 sheet: -0.73 (0.42), residues: 144 loop : -2.21 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 303 TYR 0.011 0.001 TYR B 219 PHE 0.012 0.002 PHE B 228 TRP 0.004 0.001 TRP A 353 HIS 0.003 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.19 ( 6132) covalent geometry : angle 0.57101 / 0.30 ( 8322) hydrogen bonds : bond 0.05032 / 3.22 ( 315) hydrogen bonds : angle 4.31598 / 3.05 ( 921) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.240 Fit side-chains REVERT: B 46 THR cc_start: 0.8662 (m) cc_final: 0.8390 (m) REVERT: A 17 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7294 (ttp) outliers start: 16 outliers final: 10 residues processed: 56 average time/residue: 0.0812 time to fit residues: 6.2990 Evaluate side-chains 49 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 68 optimal weight: 0.0570 chunk 65 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN A 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.167209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119830 restraints weight = 7031.770| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.02 r_work: 0.3094 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6132 Z= 0.113 Angle : 0.485 5.174 8322 Z= 0.258 Chirality : 0.043 0.157 970 Planarity : 0.004 0.044 1032 Dihedral : 18.188 151.016 912 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.36 % Allowed : 19.39 % Favored : 79.24 % 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: 0.36 (0.32), residues: 732 helix: 2.40 (0.28), residues: 330 sheet: -0.59 (0.42), residues: 142 loop : -2.25 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 303 TYR 0.009 0.001 TYR B 299 PHE 0.010 0.001 PHE B 228 TRP 0.003 0.001 TRP A 353 HIS 0.002 0.001 HIS B 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6132) covalent geometry : angle 0.48470 / 0.26 ( 8322) hydrogen bonds : bond 0.03780 / 2.41 ( 315) hydrogen bonds : angle 4.13721 / 2.92 ( 921) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.217 Fit side-chains REVERT: B 27 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.6669 (tptt) REVERT: B 46 THR cc_start: 0.8613 (m) cc_final: 0.8348 (m) REVERT: A 17 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7260 (ttp) outliers start: 9 outliers final: 4 residues processed: 54 average time/residue: 0.0937 time to fit residues: 6.6696 Evaluate side-chains 50 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN A 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118072 restraints weight = 7102.461| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.03 r_work: 0.3056 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6132 Z= 0.144 Angle : 0.519 6.309 8322 Z= 0.273 Chirality : 0.044 0.159 970 Planarity : 0.004 0.044 1032 Dihedral : 17.901 154.722 912 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.58 % Allowed : 18.79 % Favored : 78.64 % 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: 0.31 (0.31), residues: 732 helix: 2.37 (0.28), residues: 330 sheet: -0.62 (0.42), residues: 142 loop : -2.29 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 303 TYR 0.009 0.001 TYR B 219 PHE 0.013 0.001 PHE A 228 TRP 0.003 0.001 TRP B 353 HIS 0.002 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 6132) covalent geometry : angle 0.51919 / 0.27 ( 8322) hydrogen bonds : bond 0.04296 / 2.74 ( 315) hydrogen bonds : angle 4.17720 / 2.96 ( 921) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.183 Fit side-chains REVERT: B 27 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.6674 (tptt) REVERT: B 46 THR cc_start: 0.8609 (m) cc_final: 0.8352 (m) REVERT: A 17 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7268 (ttp) REVERT: A 27 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.6651 (tptt) outliers start: 17 outliers final: 13 residues processed: 55 average time/residue: 0.0924 time to fit residues: 6.7449 Evaluate side-chains 56 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.0170 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN A 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.167179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119871 restraints weight = 7005.125| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.01 r_work: 0.3012 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6132 Z= 0.113 Angle : 0.492 5.732 8322 Z= 0.260 Chirality : 0.043 0.141 970 Planarity : 0.004 0.044 1032 Dihedral : 17.570 155.263 912 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.42 % Allowed : 18.94 % Favored : 78.64 % 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: 0.37 (0.32), residues: 732 helix: 2.44 (0.28), residues: 330 sheet: -0.60 (0.42), residues: 142 loop : -2.28 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 303 TYR 0.009 0.001 TYR B 299 PHE 0.009 0.001 PHE B 228 TRP 0.002 0.001 TRP A 353 HIS 0.002 0.001 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 6132) covalent geometry : angle 0.49151 / 0.26 ( 8322) hydrogen bonds : bond 0.03813 / 2.44 ( 315) hydrogen bonds : angle 4.11895 / 2.92 ( 921) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.6621 (tptt) REVERT: A 27 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6606 (tptt) REVERT: A 171 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7384 (tp30) outliers start: 16 outliers final: 12 residues processed: 58 average time/residue: 0.1026 time to fit residues: 7.7154 Evaluate side-chains 58 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 359 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.0270 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN A 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.166842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.119442 restraints weight = 7099.609| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.03 r_work: 0.3076 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6132 Z= 0.122 Angle : 0.502 6.245 8322 Z= 0.264 Chirality : 0.043 0.138 970 Planarity : 0.004 0.044 1032 Dihedral : 17.381 157.424 912 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.73 % Allowed : 18.64 % Favored : 78.64 % 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: 0.37 (0.32), residues: 732 helix: 2.45 (0.28), residues: 330 sheet: -0.59 (0.43), residues: 142 loop : -2.30 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 303 TYR 0.008 0.001 TYR A 299 PHE 0.010 0.001 PHE B 228 TRP 0.002 0.001 TRP B 353 HIS 0.001 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 6132) covalent geometry : angle 0.50179 / 0.26 ( 8322) hydrogen bonds : bond 0.03938 / 2.52 ( 315) hydrogen bonds : angle 4.11188 / 2.92 ( 921) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.214 Fit side-chains REVERT: B 27 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.6649 (tptt) REVERT: B 171 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: A 27 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.6651 (tptt) REVERT: A 171 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7467 (tp30) outliers start: 18 outliers final: 14 residues processed: 61 average time/residue: 0.0984 time to fit residues: 7.7036 Evaluate side-chains 61 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 359 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 57 optimal weight: 0.0270 chunk 55 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN A 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.168095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120396 restraints weight = 7063.023| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.03 r_work: 0.3019 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6132 Z= 0.110 Angle : 0.487 6.033 8322 Z= 0.257 Chirality : 0.043 0.140 970 Planarity : 0.004 0.044 1032 Dihedral : 17.143 157.337 912 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.12 % Allowed : 19.24 % Favored : 78.64 % 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: 0.45 (0.32), residues: 732 helix: 2.50 (0.28), residues: 330 sheet: -0.49 (0.43), residues: 140 loop : -2.27 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 303 TYR 0.008 0.001 TYR A 299 PHE 0.008 0.001 PHE B 228 TRP 0.002 0.001 TRP A 353 HIS 0.001 0.001 HIS A 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6132) covalent geometry : angle 0.48724 / 0.26 ( 8322) hydrogen bonds : bond 0.03654 / 2.34 ( 315) hydrogen bonds : angle 4.07227 / 2.89 ( 921) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.6615 (tptt) REVERT: B 171 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: A 16 ILE cc_start: 0.7391 (mm) cc_final: 0.7003 (mt) REVERT: A 27 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.6635 (tptt) outliers start: 14 outliers final: 11 residues processed: 59 average time/residue: 0.0914 time to fit residues: 6.9300 Evaluate side-chains 59 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 359 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.166255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118666 restraints weight = 7101.947| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.03 r_work: 0.3050 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6132 Z= 0.139 Angle : 0.518 6.904 8322 Z= 0.271 Chirality : 0.044 0.146 970 Planarity : 0.004 0.044 1032 Dihedral : 17.307 160.223 912 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.03 % Allowed : 18.64 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.32), residues: 732 helix: 2.45 (0.28), residues: 330 sheet: -0.52 (0.43), residues: 140 loop : -2.30 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 303 TYR 0.009 0.001 TYR B 109 PHE 0.011 0.001 PHE B 228 TRP 0.002 0.001 TRP B 353 HIS 0.002 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 6132) covalent geometry : angle 0.51770 / 0.27 ( 8322) hydrogen bonds : bond 0.04158 / 2.66 ( 315) hydrogen bonds : angle 4.12389 / 2.93 ( 921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1875.27 seconds wall clock time: 32 minutes 47.77 seconds (1967.77 seconds total)