Starting phenix.real_space_refine on Fri Jul 3 16:06:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wbk_65842/07_2026/9wbk_65842.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wbk_65842/07_2026/9wbk_65842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wbk_65842/07_2026/9wbk_65842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wbk_65842/07_2026/9wbk_65842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wbk_65842/07_2026/9wbk_65842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wbk_65842/07_2026/9wbk_65842.map" } resolution = 3.39 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= 0.028 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 9184 2.51 5 N 2632 2.21 5 O 2800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14672 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 524 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Restraints were copied for chains: C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c Time building chain proxies: 1.33, per 1000 atoms: 0.09 Number of scatterers: 14672 At special positions: 0 Unit cell: (63.91, 63.91, 312.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 2800 8.00 N 2632 7.00 C 9184 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: 1.26 Conformation dependent library (CDL) restraints added in 515.6 milliseconds 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 0 sheets defined 88.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 284 through 294 removed outlier: 3.738A pdb=" N LEU B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 311 through 317 Processing helix chain 'B' and resid 319 through 327 Processing helix chain 'B' and resid 329 through 351 Processing helix chain 'C' and resid 285 through 294 Processing helix chain 'C' and resid 297 through 308 Processing helix chain 'C' and resid 311 through 317 Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 329 through 351 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 297 through 308 Processing helix chain 'D' and resid 311 through 317 Processing helix chain 'D' and resid 319 through 327 Processing helix chain 'D' and resid 329 through 351 Processing helix chain 'E' and resid 285 through 294 Processing helix chain 'E' and resid 297 through 308 Processing helix chain 'E' and resid 311 through 317 Processing helix chain 'E' and resid 319 through 327 Processing helix chain 'E' and resid 329 through 351 Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 297 through 308 Processing helix chain 'F' and resid 311 through 317 Processing helix chain 'F' and resid 319 through 327 Processing helix chain 'F' and resid 329 through 351 Processing helix chain 'G' and resid 285 through 294 Processing helix chain 'G' and resid 297 through 308 Processing helix chain 'G' and resid 311 through 317 Processing helix chain 'G' and resid 319 through 327 Processing helix chain 'G' and resid 329 through 351 Processing helix chain 'H' and resid 285 through 294 Processing helix chain 'H' and resid 297 through 308 Processing helix chain 'H' and resid 311 through 317 Processing helix chain 'H' and resid 319 through 327 Processing helix chain 'H' and resid 329 through 351 Processing helix chain 'I' and resid 285 through 294 Processing helix chain 'I' and resid 297 through 308 Processing helix chain 'I' and resid 311 through 317 Processing helix chain 'I' and resid 319 through 327 Processing helix chain 'I' and resid 329 through 351 Processing helix chain 'J' and resid 285 through 294 Processing helix chain 'J' and resid 297 through 308 Processing helix chain 'J' and resid 311 through 317 Processing helix chain 'J' and resid 319 through 327 Processing helix chain 'J' and resid 329 through 351 Processing helix chain 'K' and resid 285 through 294 Processing helix chain 'K' and resid 297 through 308 Processing helix chain 'K' and resid 311 through 317 Processing helix chain 'K' and resid 319 through 327 Processing helix chain 'K' and resid 329 through 351 Processing helix chain 'L' and resid 285 through 294 Processing helix chain 'L' and resid 297 through 308 Processing helix chain 'L' and resid 311 through 317 Processing helix chain 'L' and resid 319 through 327 Processing helix chain 'L' and resid 329 through 351 Processing helix chain 'M' and resid 285 through 294 Processing helix chain 'M' and resid 297 through 308 Processing helix chain 'M' and resid 311 through 317 Processing helix chain 'M' and resid 319 through 327 Processing helix chain 'M' and resid 329 through 351 Processing helix chain 'N' and resid 285 through 294 Processing helix chain 'N' and resid 297 through 308 Processing helix chain 'N' and resid 311 through 317 Processing helix chain 'N' and resid 319 through 327 Processing helix chain 'N' and resid 329 through 351 Processing helix chain 'O' and resid 285 through 294 Processing helix chain 'O' and resid 297 through 308 Processing helix chain 'O' and resid 311 through 317 Processing helix chain 'O' and resid 319 through 327 Processing helix chain 'O' and resid 329 through 351 Processing helix chain 'P' and resid 285 through 294 Processing helix chain 'P' and resid 297 through 308 Processing helix chain 'P' and resid 311 through 317 Processing helix chain 'P' and resid 319 through 327 Processing helix chain 'P' and resid 329 through 351 Processing helix chain 'Q' and resid 285 through 294 Processing helix chain 'Q' and resid 297 through 308 Processing helix chain 'Q' and resid 311 through 317 Processing helix chain 'Q' and resid 319 through 327 Processing helix chain 'Q' and resid 329 through 351 Processing helix chain 'R' and resid 285 through 294 Processing helix chain 'R' and resid 297 through 308 Processing helix chain 'R' and resid 311 through 317 Processing helix chain 'R' and resid 319 through 327 Processing helix chain 'R' and resid 329 through 351 Processing helix chain 'S' and resid 285 through 294 Processing helix chain 'S' and resid 297 through 308 Processing helix chain 'S' and resid 311 through 317 Processing helix chain 'S' and resid 319 through 327 Processing helix chain 'S' and resid 329 through 351 Processing helix chain 'T' and resid 285 through 294 Processing helix chain 'T' and resid 297 through 308 Processing helix chain 'T' and resid 311 through 317 Processing helix chain 'T' and resid 319 through 327 Processing helix chain 'T' and resid 329 through 351 Processing helix chain 'U' and resid 285 through 294 Processing helix chain 'U' and resid 297 through 308 Processing helix chain 'U' and resid 311 through 317 Processing helix chain 'U' and resid 319 through 327 Processing helix chain 'U' and resid 329 through 351 Processing helix chain 'V' and resid 285 through 294 Processing helix chain 'V' and resid 297 through 308 Processing helix chain 'V' and resid 311 through 317 Processing helix chain 'V' and resid 319 through 327 Processing helix chain 'V' and resid 329 through 351 Processing helix chain 'W' and resid 285 through 294 Processing helix chain 'W' and resid 297 through 308 Processing helix chain 'W' and resid 311 through 317 Processing helix chain 'W' and resid 319 through 327 Processing helix chain 'W' and resid 329 through 351 Processing helix chain 'X' and resid 285 through 294 Processing helix chain 'X' and resid 297 through 308 Processing helix chain 'X' and resid 311 through 317 Processing helix chain 'X' and resid 319 through 327 Processing helix chain 'X' and resid 329 through 351 Processing helix chain 'Y' and resid 285 through 294 Processing helix chain 'Y' and resid 297 through 308 Processing helix chain 'Y' and resid 311 through 317 Processing helix chain 'Y' and resid 319 through 327 Processing helix chain 'Y' and resid 329 through 351 Processing helix chain 'Z' and resid 285 through 294 Processing helix chain 'Z' and resid 297 through 308 Processing helix chain 'Z' and resid 311 through 317 Processing helix chain 'Z' and resid 319 through 327 Processing helix chain 'Z' and resid 329 through 351 Processing helix chain 'a' and resid 285 through 294 Processing helix chain 'a' and resid 297 through 308 Processing helix chain 'a' and resid 311 through 317 Processing helix chain 'a' and resid 319 through 327 Processing helix chain 'a' and resid 329 through 351 Processing helix chain 'b' and resid 285 through 294 Processing helix chain 'b' and resid 297 through 308 Processing helix chain 'b' and resid 311 through 317 Processing helix chain 'b' and resid 319 through 327 Processing helix chain 'b' and resid 329 through 351 Processing helix chain 'c' and resid 285 through 294 Processing helix chain 'c' and resid 297 through 308 Processing helix chain 'c' and resid 311 through 317 Processing helix chain 'c' and resid 319 through 327 Processing helix chain 'c' and resid 329 through 351 1148 hydrogen bonds defined for protein. 3444 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5124 1.34 - 1.46: 2786 1.46 - 1.58: 6846 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 14840 Sorted by residual: bond pdb=" C ALA Y 333 " pdb=" N ARG Y 334 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.43e-02 4.89e+03 1.14e+00 bond pdb=" C ALA C 333 " pdb=" N ARG C 334 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.43e-02 4.89e+03 1.09e+00 bond pdb=" C ALA E 333 " pdb=" N ARG E 334 " ideal model delta sigma weight residual 1.334 1.320 0.015 1.43e-02 4.89e+03 1.06e+00 bond pdb=" C ALA X 333 " pdb=" N ARG X 334 " ideal model delta sigma weight residual 1.334 1.320 0.015 1.43e-02 4.89e+03 1.06e+00 bond pdb=" C ALA O 333 " pdb=" N ARG O 334 " ideal model delta sigma weight residual 1.334 1.320 0.015 1.43e-02 4.89e+03 1.06e+00 ... (remaining 14835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 18499 1.30 - 2.59: 1190 2.59 - 3.89: 274 3.89 - 5.18: 57 5.18 - 6.48: 56 Bond angle restraints: 20076 Sorted by residual: angle pdb=" CB ARG S 334 " pdb=" CG ARG S 334 " pdb=" CD ARG S 334 " ideal model delta sigma weight residual 111.30 106.47 4.83 2.30e+00 1.89e-01 4.40e+00 angle pdb=" CB ARG U 334 " pdb=" CG ARG U 334 " pdb=" CD ARG U 334 " ideal model delta sigma weight residual 111.30 106.48 4.82 2.30e+00 1.89e-01 4.39e+00 angle pdb=" CB ARG D 334 " pdb=" CG ARG D 334 " pdb=" CD ARG D 334 " ideal model delta sigma weight residual 111.30 106.48 4.82 2.30e+00 1.89e-01 4.38e+00 angle pdb=" CB ARG X 334 " pdb=" CG ARG X 334 " pdb=" CD ARG X 334 " ideal model delta sigma weight residual 111.30 106.49 4.81 2.30e+00 1.89e-01 4.37e+00 angle pdb=" CB ARG M 334 " pdb=" CG ARG M 334 " pdb=" CD ARG M 334 " ideal model delta sigma weight residual 111.30 106.50 4.80 2.30e+00 1.89e-01 4.36e+00 ... (remaining 20071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 8372 15.88 - 31.75: 699 31.75 - 47.63: 57 47.63 - 63.50: 56 63.50 - 79.38: 56 Dihedral angle restraints: 9240 sinusoidal: 3612 harmonic: 5628 Sorted by residual: dihedral pdb=" CA GLY T 295 " pdb=" C GLY T 295 " pdb=" N VAL T 296 " pdb=" CA VAL T 296 " ideal model delta harmonic sigma weight residual 180.00 165.94 14.06 0 5.00e+00 4.00e-02 7.91e+00 dihedral pdb=" CA GLY c 295 " pdb=" C GLY c 295 " pdb=" N VAL c 296 " pdb=" CA VAL c 296 " ideal model delta harmonic sigma weight residual 180.00 165.94 14.06 0 5.00e+00 4.00e-02 7.91e+00 dihedral pdb=" CA GLY S 295 " pdb=" C GLY S 295 " pdb=" N VAL S 296 " pdb=" CA VAL S 296 " ideal model delta harmonic sigma weight residual 180.00 165.94 14.06 0 5.00e+00 4.00e-02 7.90e+00 ... (remaining 9237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1064 0.027 - 0.055: 788 0.055 - 0.082: 332 0.082 - 0.109: 140 0.109 - 0.137: 56 Chirality restraints: 2380 Sorted by residual: chirality pdb=" CG LEU I 304 " pdb=" CB LEU I 304 " pdb=" CD1 LEU I 304 " pdb=" CD2 LEU I 304 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CG LEU C 304 " pdb=" CB LEU C 304 " pdb=" CD1 LEU C 304 " pdb=" CD2 LEU C 304 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CG LEU b 304 " pdb=" CB LEU b 304 " pdb=" CD1 LEU b 304 " pdb=" CD2 LEU b 304 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 2377 not shown) Planarity restraints: 2660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 311 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO I 312 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO I 312 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 312 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER a 311 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO a 312 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO a 312 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO a 312 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER P 311 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO P 312 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO P 312 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO P 312 " 0.021 5.00e-02 4.00e+02 ... (remaining 2657 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 354 2.66 - 3.22: 15670 3.22 - 3.78: 24829 3.78 - 4.34: 31468 4.34 - 4.90: 48401 Nonbonded interactions: 120722 Sorted by model distance: nonbonded pdb=" OD2 ASP V 322 " pdb=" NH1 ARG a 334 " model vdw 2.098 3.120 nonbonded pdb=" NH1 ARG D 334 " pdb=" OD2 ASP E 322 " model vdw 2.125 3.120 nonbonded pdb=" NH1 ARG X 334 " pdb=" OD2 ASP Y 322 " model vdw 2.148 3.120 nonbonded pdb=" NH1 ARG S 334 " pdb=" OD2 ASP T 322 " model vdw 2.150 3.120 nonbonded pdb=" OD2 ASP B 322 " pdb=" NH1 ARG C 334 " model vdw 2.160 3.120 ... (remaining 120717 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 5.890 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.220 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 0.005 0.028 14840 Z= 0.277 Angle : 0.811 6.476 20076 Z= 0.442 Chirality : 0.046 0.137 2380 Planarity : 0.005 0.037 2660 Dihedral : 14.269 79.380 5544 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1876 helix: 1.34 (0.13), residues: 1764 sheet: None (None), residues: 0 loop : -5.68 (0.22), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 334 TYR 0.002 0.001 TYR Q 284 PHE 0.007 0.002 PHE c 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.28 (14840) covalent geometry : angle 0.81126 / 0.44 (20076) hydrogen bonds : bond 0.06321 / 4.20 ( 1148) hydrogen bonds : angle 5.26081 / 3.62 ( 3444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 758 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 GLU cc_start: 0.7974 (pm20) cc_final: 0.7688 (pm20) REVERT: B 305 LEU cc_start: 0.8767 (mm) cc_final: 0.8550 (mm) REVERT: B 307 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7991 (mm-40) REVERT: B 332 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7545 (mm-40) REVERT: B 334 ARG cc_start: 0.8308 (ttm170) cc_final: 0.7935 (ttm170) REVERT: B 337 SER cc_start: 0.9098 (m) cc_final: 0.8625 (p) REVERT: C 294 GLU cc_start: 0.7789 (mp0) cc_final: 0.7327 (mp0) REVERT: C 307 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7945 (mm-40) REVERT: C 318 LEU cc_start: 0.8856 (tp) cc_final: 0.8653 (tp) REVERT: C 322 ASP cc_start: 0.7576 (m-30) cc_final: 0.7276 (m-30) REVERT: C 323 ILE cc_start: 0.8784 (mt) cc_final: 0.8581 (mm) REVERT: C 336 LEU cc_start: 0.9078 (tp) cc_final: 0.8812 (tp) REVERT: C 337 SER cc_start: 0.9022 (m) cc_final: 0.8609 (p) REVERT: C 347 MET cc_start: 0.7715 (tpp) cc_final: 0.7406 (tpp) REVERT: D 307 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7910 (mm-40) REVERT: D 318 LEU cc_start: 0.8720 (tp) cc_final: 0.8457 (tp) REVERT: D 323 ILE cc_start: 0.8715 (mt) cc_final: 0.8459 (mm) REVERT: D 330 LEU cc_start: 0.8929 (tt) cc_final: 0.8663 (tp) REVERT: D 332 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8111 (mm-40) REVERT: D 337 SER cc_start: 0.9059 (m) cc_final: 0.8716 (p) REVERT: E 290 LEU cc_start: 0.8422 (tt) cc_final: 0.7723 (tt) REVERT: E 294 GLU cc_start: 0.7698 (mp0) cc_final: 0.7235 (mp0) REVERT: E 301 LEU cc_start: 0.8824 (tp) cc_final: 0.8512 (tp) REVERT: E 307 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8077 (mm-40) REVERT: E 318 LEU cc_start: 0.8967 (tp) cc_final: 0.8747 (tp) REVERT: E 324 LYS cc_start: 0.8658 (tmtt) cc_final: 0.8359 (tmtt) REVERT: E 329 ASN cc_start: 0.8364 (p0) cc_final: 0.8115 (p0) REVERT: E 337 SER cc_start: 0.8927 (m) cc_final: 0.8598 (p) REVERT: F 298 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7069 (mm-30) REVERT: F 315 LEU cc_start: 0.8624 (tt) cc_final: 0.8396 (tt) REVERT: F 332 GLN cc_start: 0.8274 (mm-40) cc_final: 0.8011 (mm110) REVERT: F 337 SER cc_start: 0.9131 (m) cc_final: 0.8538 (t) REVERT: F 341 SER cc_start: 0.8860 (m) cc_final: 0.8383 (p) REVERT: G 292 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7873 (mtt90) REVERT: G 301 LEU cc_start: 0.8470 (tp) cc_final: 0.8243 (tp) REVERT: G 318 LEU cc_start: 0.8692 (tp) cc_final: 0.8427 (tp) REVERT: G 322 ASP cc_start: 0.7704 (m-30) cc_final: 0.7452 (m-30) REVERT: G 330 LEU cc_start: 0.8808 (tt) cc_final: 0.8570 (tt) REVERT: G 332 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7745 (mm110) REVERT: G 334 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7554 (mtp85) REVERT: G 337 SER cc_start: 0.9152 (m) cc_final: 0.8548 (t) REVERT: G 341 SER cc_start: 0.8729 (m) cc_final: 0.8457 (p) REVERT: H 287 PHE cc_start: 0.8630 (t80) cc_final: 0.8293 (t80) REVERT: H 288 LEU cc_start: 0.8319 (mp) cc_final: 0.7677 (mp) REVERT: H 292 ARG cc_start: 0.7875 (mtt90) cc_final: 0.7380 (mtt90) REVERT: H 301 LEU cc_start: 0.8488 (tp) cc_final: 0.8071 (tp) REVERT: H 305 LEU cc_start: 0.8671 (mm) cc_final: 0.8463 (mm) REVERT: H 312 PRO cc_start: 0.8768 (Cg_exo) cc_final: 0.8557 (Cg_endo) REVERT: H 322 ASP cc_start: 0.7624 (m-30) cc_final: 0.7317 (m-30) REVERT: H 324 LYS cc_start: 0.8756 (tmtt) cc_final: 0.8436 (tmtt) REVERT: H 330 LEU cc_start: 0.8599 (tt) cc_final: 0.8398 (tp) REVERT: H 332 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7888 (mm-40) REVERT: H 341 SER cc_start: 0.8578 (m) cc_final: 0.8256 (p) REVERT: I 288 LEU cc_start: 0.8620 (mp) cc_final: 0.7933 (mp) REVERT: I 292 ARG cc_start: 0.8322 (mtt90) cc_final: 0.7813 (mtt90) REVERT: I 304 LEU cc_start: 0.8669 (mm) cc_final: 0.8389 (mm) REVERT: I 318 LEU cc_start: 0.8620 (tp) cc_final: 0.8316 (tp) REVERT: I 324 LYS cc_start: 0.8821 (tmtt) cc_final: 0.8493 (tmtt) REVERT: I 336 LEU cc_start: 0.8236 (tp) cc_final: 0.8015 (tp) REVERT: J 305 LEU cc_start: 0.8810 (mm) cc_final: 0.8606 (mm) REVERT: J 307 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8165 (mm-40) REVERT: J 322 ASP cc_start: 0.7675 (m-30) cc_final: 0.7369 (m-30) REVERT: J 334 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7508 (ttm170) REVERT: J 337 SER cc_start: 0.9098 (m) cc_final: 0.8880 (m) REVERT: K 292 ARG cc_start: 0.8460 (mtt90) cc_final: 0.8222 (mtt-85) REVERT: K 298 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7368 (mm-30) REVERT: K 307 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7974 (mm110) REVERT: K 322 ASP cc_start: 0.7771 (m-30) cc_final: 0.7459 (m-30) REVERT: L 290 LEU cc_start: 0.8610 (tt) cc_final: 0.7828 (tt) REVERT: L 294 GLU cc_start: 0.7793 (mp0) cc_final: 0.7113 (mp0) REVERT: L 312 PRO cc_start: 0.8587 (Cg_exo) cc_final: 0.8257 (Cg_endo) REVERT: L 318 LEU cc_start: 0.8910 (tp) cc_final: 0.8567 (tp) REVERT: L 322 ASP cc_start: 0.7761 (m-30) cc_final: 0.7320 (m-30) REVERT: L 332 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8109 (mm110) REVERT: L 337 SER cc_start: 0.9057 (m) cc_final: 0.8765 (m) REVERT: M 292 ARG cc_start: 0.8457 (mtt90) cc_final: 0.8251 (mtt-85) REVERT: M 298 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7221 (mm-30) REVERT: M 305 LEU cc_start: 0.8773 (mm) cc_final: 0.8501 (mm) REVERT: M 330 LEU cc_start: 0.8709 (tt) cc_final: 0.8445 (tt) REVERT: M 337 SER cc_start: 0.8996 (m) cc_final: 0.8778 (m) REVERT: M 350 ARG cc_start: 0.8021 (ttm170) cc_final: 0.7754 (ttm170) REVERT: N 305 LEU cc_start: 0.8759 (mm) cc_final: 0.8558 (mm) REVERT: N 307 GLN cc_start: 0.8248 (mm-40) cc_final: 0.8014 (mt0) REVERT: O 292 ARG cc_start: 0.8508 (mtt90) cc_final: 0.8290 (mtt-85) REVERT: P 290 LEU cc_start: 0.8491 (tt) cc_final: 0.7761 (tt) REVERT: P 292 ARG cc_start: 0.8549 (mtt90) cc_final: 0.8336 (mtt90) REVERT: P 294 GLU cc_start: 0.7718 (mp0) cc_final: 0.7055 (mp0) REVERT: P 312 PRO cc_start: 0.8690 (Cg_exo) cc_final: 0.8444 (Cg_endo) REVERT: P 324 LYS cc_start: 0.8769 (tmtt) cc_final: 0.8523 (tmtt) REVERT: P 337 SER cc_start: 0.9175 (m) cc_final: 0.8906 (m) REVERT: Q 298 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6824 (mm-30) REVERT: Q 312 PRO cc_start: 0.8668 (Cg_exo) cc_final: 0.8295 (Cg_endo) REVERT: Q 339 LEU cc_start: 0.8449 (mm) cc_final: 0.7901 (mm) REVERT: Q 343 CYS cc_start: 0.7738 (m) cc_final: 0.7386 (m) REVERT: R 298 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7371 (mm-30) REVERT: R 305 LEU cc_start: 0.8919 (mm) cc_final: 0.8698 (mm) REVERT: R 307 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8045 (mm-40) REVERT: R 323 ILE cc_start: 0.8706 (mt) cc_final: 0.8485 (mm) REVERT: R 337 SER cc_start: 0.9073 (m) cc_final: 0.8545 (t) REVERT: S 298 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7578 (mm-30) REVERT: S 307 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8279 (mm-40) REVERT: S 317 THR cc_start: 0.8346 (m) cc_final: 0.8019 (t) REVERT: S 318 LEU cc_start: 0.8718 (tp) cc_final: 0.8452 (tp) REVERT: S 332 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7902 (mm110) REVERT: S 337 SER cc_start: 0.9065 (m) cc_final: 0.8741 (m) REVERT: S 341 SER cc_start: 0.8680 (m) cc_final: 0.8315 (p) REVERT: T 288 LEU cc_start: 0.8346 (mp) cc_final: 0.7937 (mp) REVERT: T 292 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7696 (mtt90) REVERT: T 324 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8432 (tmtt) REVERT: T 334 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7522 (mmm-85) REVERT: U 288 LEU cc_start: 0.8620 (mp) cc_final: 0.7983 (mp) REVERT: U 292 ARG cc_start: 0.8454 (mtt90) cc_final: 0.7907 (mtt90) REVERT: U 301 LEU cc_start: 0.8760 (tp) cc_final: 0.8234 (tp) REVERT: U 305 LEU cc_start: 0.8708 (mm) cc_final: 0.8424 (mm) REVERT: U 334 ARG cc_start: 0.7968 (ttm170) cc_final: 0.7446 (mmm-85) REVERT: U 336 LEU cc_start: 0.8514 (tp) cc_final: 0.8308 (tp) REVERT: V 286 GLU cc_start: 0.7400 (pm20) cc_final: 0.7196 (pm20) REVERT: V 322 ASP cc_start: 0.7503 (m-30) cc_final: 0.7086 (m-30) REVERT: V 323 ILE cc_start: 0.8803 (mt) cc_final: 0.8564 (mm) REVERT: V 334 ARG cc_start: 0.7789 (ttm170) cc_final: 0.7357 (ttm170) REVERT: V 336 LEU cc_start: 0.8969 (tp) cc_final: 0.8650 (tp) REVERT: V 337 SER cc_start: 0.9028 (m) cc_final: 0.8616 (p) REVERT: V 348 GLN cc_start: 0.8318 (mt0) cc_final: 0.7925 (mt0) REVERT: W 286 GLU cc_start: 0.7981 (pm20) cc_final: 0.7679 (pm20) REVERT: W 307 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7975 (mm-40) REVERT: W 318 LEU cc_start: 0.8784 (tp) cc_final: 0.8530 (tp) REVERT: W 338 ARG cc_start: 0.7896 (tpp80) cc_final: 0.7018 (tpp80) REVERT: W 350 ARG cc_start: 0.7701 (ttm170) cc_final: 0.7023 (ttm170) REVERT: X 305 LEU cc_start: 0.8898 (mm) cc_final: 0.8669 (mm) REVERT: X 307 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8126 (mm-40) REVERT: X 318 LEU cc_start: 0.8783 (tp) cc_final: 0.8553 (tp) REVERT: X 322 ASP cc_start: 0.7576 (m-30) cc_final: 0.7222 (m-30) REVERT: X 337 SER cc_start: 0.8875 (m) cc_final: 0.8568 (p) REVERT: Y 301 LEU cc_start: 0.8751 (tp) cc_final: 0.8412 (tp) REVERT: Y 305 LEU cc_start: 0.8909 (mm) cc_final: 0.8679 (mm) REVERT: Z 309 PHE cc_start: 0.7496 (m-80) cc_final: 0.7279 (m-80) REVERT: Z 318 LEU cc_start: 0.8460 (tp) cc_final: 0.8092 (tp) REVERT: Z 322 ASP cc_start: 0.7529 (m-30) cc_final: 0.7290 (m-30) REVERT: Z 334 ARG cc_start: 0.8607 (ttm170) cc_final: 0.8168 (ttm-80) REVERT: Z 337 SER cc_start: 0.8827 (m) cc_final: 0.8528 (p) REVERT: Z 338 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7789 (mmm-85) REVERT: Z 347 MET cc_start: 0.7724 (tpp) cc_final: 0.7228 (tpp) REVERT: Z 348 GLN cc_start: 0.8069 (mt0) cc_final: 0.7867 (mt0) REVERT: a 291 LEU cc_start: 0.8730 (mp) cc_final: 0.8423 (mp) REVERT: a 322 ASP cc_start: 0.8027 (m-30) cc_final: 0.7726 (m-30) REVERT: a 347 MET cc_start: 0.7865 (tpp) cc_final: 0.6954 (tpp) REVERT: b 318 LEU cc_start: 0.8815 (tp) cc_final: 0.8505 (mt) REVERT: c 307 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8042 (mm-40) REVERT: c 334 ARG cc_start: 0.8725 (ttm170) cc_final: 0.8431 (ttm170) REVERT: c 337 SER cc_start: 0.8857 (m) cc_final: 0.8632 (p) REVERT: c 347 MET cc_start: 0.7786 (tpp) cc_final: 0.7424 (tpp) outliers start: 0 outliers final: 0 residues processed: 758 average time/residue: 0.1463 time to fit residues: 153.9894 Evaluate side-chains 752 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 752 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0170 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 332 GLN Q 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.126088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111687 restraints weight = 25270.263| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.31 r_work: 0.3486 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14840 Z= 0.156 Angle : 0.738 7.827 20076 Z= 0.342 Chirality : 0.041 0.175 2380 Planarity : 0.005 0.073 2660 Dihedral : 4.542 15.974 2100 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 3.70 % Allowed : 12.70 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.21), residues: 1876 helix: 2.05 (0.13), residues: 1736 sheet: None (None), residues: 0 loop : -3.96 (0.32), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 344 TYR 0.003 0.000 TYR V 284 PHE 0.011 0.001 PHE c 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (14840) covalent geometry : angle 0.73796 / 0.34 (20076) hydrogen bonds : bond 0.03070 / 2.08 ( 1148) hydrogen bonds : angle 4.09974 / 2.85 ( 3444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 723 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 GLU cc_start: 0.8242 (pm20) cc_final: 0.7948 (pm20) REVERT: B 291 LEU cc_start: 0.8730 (mp) cc_final: 0.8350 (mp) REVERT: B 305 LEU cc_start: 0.8860 (mm) cc_final: 0.8591 (mm) REVERT: B 323 ILE cc_start: 0.8990 (mt) cc_final: 0.8789 (mp) REVERT: B 332 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7876 (mm110) REVERT: B 334 ARG cc_start: 0.8552 (ttm170) cc_final: 0.7820 (mmm-85) REVERT: B 337 SER cc_start: 0.9097 (m) cc_final: 0.8643 (p) REVERT: B 338 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7699 (tpp80) REVERT: C 290 LEU cc_start: 0.8415 (tt) cc_final: 0.7873 (tt) REVERT: C 294 GLU cc_start: 0.8125 (mp0) cc_final: 0.7492 (mp0) REVERT: C 307 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7979 (mm-40) REVERT: C 318 LEU cc_start: 0.8988 (tp) cc_final: 0.8713 (tp) REVERT: C 322 ASP cc_start: 0.8305 (m-30) cc_final: 0.8068 (m-30) REVERT: C 336 LEU cc_start: 0.9196 (tp) cc_final: 0.8995 (tp) REVERT: C 344 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7796 (ttm110) REVERT: C 347 MET cc_start: 0.8423 (tpp) cc_final: 0.7940 (tpp) REVERT: D 291 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8573 (tp) REVERT: D 307 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8272 (mm-40) REVERT: D 315 LEU cc_start: 0.8592 (tt) cc_final: 0.8365 (tt) REVERT: D 318 LEU cc_start: 0.8836 (tp) cc_final: 0.8545 (tp) REVERT: D 322 ASP cc_start: 0.8148 (m-30) cc_final: 0.7896 (m-30) REVERT: D 323 ILE cc_start: 0.8791 (mt) cc_final: 0.8585 (mt) REVERT: D 337 SER cc_start: 0.8944 (m) cc_final: 0.8648 (p) REVERT: D 350 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7916 (ttm170) REVERT: E 286 GLU cc_start: 0.8186 (pm20) cc_final: 0.7781 (pm20) REVERT: E 298 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7793 (mm-30) REVERT: E 301 LEU cc_start: 0.8869 (tp) cc_final: 0.8561 (tp) REVERT: E 307 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8482 (mm-40) REVERT: E 318 LEU cc_start: 0.9030 (tp) cc_final: 0.8657 (tp) REVERT: E 329 ASN cc_start: 0.8270 (p0) cc_final: 0.8002 (p0) REVERT: E 347 MET cc_start: 0.8250 (tpp) cc_final: 0.7991 (mpp) REVERT: F 337 SER cc_start: 0.9034 (m) cc_final: 0.8574 (t) REVERT: F 341 SER cc_start: 0.8977 (m) cc_final: 0.8349 (p) REVERT: G 292 ARG cc_start: 0.8383 (mtt90) cc_final: 0.8033 (mtt90) REVERT: G 301 LEU cc_start: 0.8652 (tp) cc_final: 0.8444 (tp) REVERT: G 312 PRO cc_start: 0.8691 (Cg_exo) cc_final: 0.8227 (Cg_endo) REVERT: G 318 LEU cc_start: 0.8835 (tp) cc_final: 0.8582 (tp) REVERT: G 322 ASP cc_start: 0.8390 (m-30) cc_final: 0.7919 (m-30) REVERT: G 323 ILE cc_start: 0.8801 (mt) cc_final: 0.8557 (mt) REVERT: G 330 LEU cc_start: 0.8814 (tt) cc_final: 0.8553 (tt) REVERT: G 332 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8099 (mm-40) REVERT: G 334 ARG cc_start: 0.8654 (ttm170) cc_final: 0.7804 (mtp85) REVERT: G 337 SER cc_start: 0.8950 (m) cc_final: 0.8495 (t) REVERT: G 341 SER cc_start: 0.8888 (m) cc_final: 0.8618 (p) REVERT: G 347 MET cc_start: 0.8170 (tpp) cc_final: 0.7546 (mpp) REVERT: H 287 PHE cc_start: 0.8733 (t80) cc_final: 0.8510 (t80) REVERT: H 301 LEU cc_start: 0.8736 (tp) cc_final: 0.8346 (tp) REVERT: H 305 LEU cc_start: 0.8924 (mm) cc_final: 0.8634 (mm) REVERT: H 312 PRO cc_start: 0.8796 (Cg_exo) cc_final: 0.8413 (Cg_endo) REVERT: H 322 ASP cc_start: 0.8419 (m-30) cc_final: 0.8039 (m-30) REVERT: H 347 MET cc_start: 0.8386 (tpp) cc_final: 0.7850 (mpp) REVERT: I 288 LEU cc_start: 0.8705 (mp) cc_final: 0.8124 (mp) REVERT: I 292 ARG cc_start: 0.8649 (mtt90) cc_final: 0.8185 (mtt90) REVERT: I 304 LEU cc_start: 0.8779 (mm) cc_final: 0.8504 (mm) REVERT: I 318 LEU cc_start: 0.8903 (tp) cc_final: 0.8652 (tp) REVERT: I 324 LYS cc_start: 0.8918 (tmtt) cc_final: 0.8549 (tmtt) REVERT: I 348 GLN cc_start: 0.8198 (mt0) cc_final: 0.7930 (mt0) REVERT: J 286 GLU cc_start: 0.8382 (pm20) cc_final: 0.8096 (pm20) REVERT: J 301 LEU cc_start: 0.8872 (tp) cc_final: 0.8647 (tp) REVERT: J 307 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8377 (mm-40) REVERT: J 322 ASP cc_start: 0.8261 (m-30) cc_final: 0.7968 (m-30) REVERT: J 337 SER cc_start: 0.8960 (m) cc_final: 0.8586 (p) REVERT: K 292 ARG cc_start: 0.8767 (mtt90) cc_final: 0.8335 (mtt-85) REVERT: K 307 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8524 (mm110) REVERT: K 322 ASP cc_start: 0.8378 (m-30) cc_final: 0.8023 (m-30) REVERT: K 323 ILE cc_start: 0.8819 (mt) cc_final: 0.8468 (mm) REVERT: K 344 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8454 (ttp-110) REVERT: L 307 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8576 (mm110) REVERT: L 318 LEU cc_start: 0.9036 (tp) cc_final: 0.8737 (tp) REVERT: L 322 ASP cc_start: 0.8336 (m-30) cc_final: 0.7998 (m-30) REVERT: L 337 SER cc_start: 0.8832 (m) cc_final: 0.8497 (m) REVERT: L 350 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8195 (ttm110) REVERT: M 286 GLU cc_start: 0.8273 (pm20) cc_final: 0.7969 (pm20) REVERT: M 305 LEU cc_start: 0.8926 (mm) cc_final: 0.8615 (mm) REVERT: M 330 LEU cc_start: 0.8757 (tt) cc_final: 0.8539 (tt) REVERT: M 334 ARG cc_start: 0.8844 (ttm170) cc_final: 0.8619 (ttm170) REVERT: M 337 SER cc_start: 0.8943 (m) cc_final: 0.8719 (m) REVERT: N 305 LEU cc_start: 0.8917 (mm) cc_final: 0.8700 (mm) REVERT: N 307 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8121 (mm-40) REVERT: N 347 MET cc_start: 0.8325 (tpp) cc_final: 0.8051 (mpp) REVERT: O 298 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8092 (mm-30) REVERT: O 307 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8614 (mm110) REVERT: O 329 ASN cc_start: 0.8205 (p0) cc_final: 0.7918 (p0) REVERT: O 343 CYS cc_start: 0.8344 (m) cc_final: 0.8021 (m) REVERT: P 290 LEU cc_start: 0.8431 (tt) cc_final: 0.7948 (tt) REVERT: P 294 GLU cc_start: 0.8242 (mp0) cc_final: 0.7573 (mp0) REVERT: P 337 SER cc_start: 0.8997 (m) cc_final: 0.8686 (m) REVERT: P 347 MET cc_start: 0.8321 (tpp) cc_final: 0.7892 (mpp) REVERT: Q 322 ASP cc_start: 0.8483 (m-30) cc_final: 0.8094 (m-30) REVERT: Q 339 LEU cc_start: 0.8633 (mm) cc_final: 0.8224 (mm) REVERT: Q 343 CYS cc_start: 0.8527 (m) cc_final: 0.8111 (m) REVERT: R 307 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8256 (mm-40) REVERT: R 337 SER cc_start: 0.8905 (m) cc_final: 0.8423 (t) REVERT: R 350 ARG cc_start: 0.8583 (ttm170) cc_final: 0.8353 (ttm170) REVERT: S 291 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8434 (tp) REVERT: S 298 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7898 (mm-30) REVERT: S 318 LEU cc_start: 0.8804 (tp) cc_final: 0.8528 (tp) REVERT: S 325 SER cc_start: 0.9084 (t) cc_final: 0.8798 (p) REVERT: S 334 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.7926 (mtt90) REVERT: S 337 SER cc_start: 0.8816 (m) cc_final: 0.8501 (m) REVERT: S 341 SER cc_start: 0.8745 (m) cc_final: 0.8372 (p) REVERT: T 292 ARG cc_start: 0.8511 (mtt90) cc_final: 0.7954 (mtt90) REVERT: T 301 LEU cc_start: 0.8647 (tp) cc_final: 0.8421 (tp) REVERT: T 322 ASP cc_start: 0.8139 (m-30) cc_final: 0.7485 (m-30) REVERT: T 334 ARG cc_start: 0.8328 (ttm170) cc_final: 0.7995 (mmm-85) REVERT: T 347 MET cc_start: 0.8513 (tpp) cc_final: 0.7858 (tpp) REVERT: U 288 LEU cc_start: 0.8698 (mp) cc_final: 0.8127 (mp) REVERT: U 292 ARG cc_start: 0.8710 (mtt90) cc_final: 0.8265 (mtt90) REVERT: U 301 LEU cc_start: 0.8830 (tp) cc_final: 0.8305 (tp) REVERT: U 305 LEU cc_start: 0.8764 (mm) cc_final: 0.8470 (mm) REVERT: U 344 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7581 (ttm170) REVERT: V 286 GLU cc_start: 0.7847 (pm20) cc_final: 0.7601 (pm20) REVERT: V 322 ASP cc_start: 0.8206 (m-30) cc_final: 0.7889 (m-30) REVERT: V 334 ARG cc_start: 0.8356 (ttm170) cc_final: 0.7820 (ttm170) REVERT: V 336 LEU cc_start: 0.9058 (tp) cc_final: 0.8786 (tp) REVERT: V 337 SER cc_start: 0.9072 (m) cc_final: 0.8740 (p) REVERT: V 344 ARG cc_start: 0.8049 (ttp-110) cc_final: 0.7717 (ttp-110) REVERT: V 348 GLN cc_start: 0.8640 (mt0) cc_final: 0.8173 (mt0) REVERT: W 286 GLU cc_start: 0.8236 (pm20) cc_final: 0.7968 (pm20) REVERT: W 322 ASP cc_start: 0.8417 (m-30) cc_final: 0.8184 (m-30) REVERT: W 323 ILE cc_start: 0.8969 (mt) cc_final: 0.8743 (mp) REVERT: W 338 ARG cc_start: 0.8446 (tpp80) cc_final: 0.7486 (tpp80) REVERT: W 347 MET cc_start: 0.8475 (tpp) cc_final: 0.8061 (mpp) REVERT: X 305 LEU cc_start: 0.9043 (mm) cc_final: 0.8798 (mm) REVERT: X 307 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8274 (mm-40) REVERT: X 322 ASP cc_start: 0.8244 (m-30) cc_final: 0.7899 (m-30) REVERT: X 337 SER cc_start: 0.8774 (m) cc_final: 0.8517 (p) REVERT: Y 286 GLU cc_start: 0.8395 (pm20) cc_final: 0.8112 (pm20) REVERT: Y 292 ARG cc_start: 0.8718 (mtt90) cc_final: 0.8285 (tpp80) REVERT: Y 301 LEU cc_start: 0.8840 (tp) cc_final: 0.8424 (tp) REVERT: Y 305 LEU cc_start: 0.9043 (mm) cc_final: 0.8735 (mm) REVERT: Z 318 LEU cc_start: 0.8651 (tp) cc_final: 0.8369 (tp) REVERT: Z 322 ASP cc_start: 0.8221 (m-30) cc_final: 0.8018 (m-30) REVERT: Z 334 ARG cc_start: 0.8584 (ttm170) cc_final: 0.8152 (ttm-80) REVERT: Z 337 SER cc_start: 0.8807 (m) cc_final: 0.8565 (p) REVERT: Z 338 ARG cc_start: 0.8643 (tpp80) cc_final: 0.8332 (tpp80) REVERT: Z 347 MET cc_start: 0.8183 (tpp) cc_final: 0.7633 (tpp) REVERT: Z 348 GLN cc_start: 0.8351 (mt0) cc_final: 0.8060 (mt0) REVERT: a 291 LEU cc_start: 0.8832 (mp) cc_final: 0.8536 (mp) REVERT: a 347 MET cc_start: 0.8140 (tpp) cc_final: 0.7266 (tpp) REVERT: b 318 LEU cc_start: 0.8804 (tp) cc_final: 0.8438 (mt) REVERT: c 334 ARG cc_start: 0.8728 (ttm170) cc_final: 0.8357 (ttm-80) outliers start: 56 outliers final: 31 residues processed: 724 average time/residue: 0.1532 time to fit residues: 152.4452 Evaluate side-chains 754 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 720 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain K residue 304 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 350 ARG Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain O residue 339 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 350 ARG Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain S residue 290 LEU Chi-restraints excluded: chain S residue 291 LEU Chi-restraints excluded: chain S residue 304 LEU Chi-restraints excluded: chain S residue 339 LEU Chi-restraints excluded: chain T residue 291 LEU Chi-restraints excluded: chain T residue 304 LEU Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 304 LEU Chi-restraints excluded: chain W residue 290 LEU Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain Y residue 339 LEU Chi-restraints excluded: chain a residue 304 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 164 optimal weight: 0.4980 chunk 116 optimal weight: 0.0270 chunk 83 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 GLN ** F 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN Q 332 GLN T 307 GLN ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.126644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110390 restraints weight = 25489.248| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.27 r_work: 0.3488 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14840 Z= 0.135 Angle : 0.694 7.984 20076 Z= 0.321 Chirality : 0.039 0.215 2380 Planarity : 0.005 0.049 2660 Dihedral : 4.261 16.878 2100 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 4.50 % Allowed : 18.06 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.20), residues: 1876 helix: 1.99 (0.13), residues: 1764 sheet: None (None), residues: 0 loop : -5.80 (0.19), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 344 TYR 0.003 0.000 TYR D 284 PHE 0.015 0.001 PHE c 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14840) covalent geometry : angle 0.69404 / 0.32 (20076) hydrogen bonds : bond 0.02825 / 1.92 ( 1148) hydrogen bonds : angle 3.75289 / 2.62 ( 3444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 713 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 GLU cc_start: 0.8132 (pm20) cc_final: 0.7854 (pm20) REVERT: B 305 LEU cc_start: 0.8891 (mm) cc_final: 0.8602 (mm) REVERT: B 332 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7758 (mm110) REVERT: B 334 ARG cc_start: 0.8564 (ttm170) cc_final: 0.8097 (ttm170) REVERT: B 337 SER cc_start: 0.9094 (m) cc_final: 0.8662 (p) REVERT: C 290 LEU cc_start: 0.8405 (tt) cc_final: 0.7860 (tt) REVERT: C 294 GLU cc_start: 0.8146 (mp0) cc_final: 0.7471 (mp0) REVERT: C 307 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8039 (mm-40) REVERT: C 318 LEU cc_start: 0.8976 (tp) cc_final: 0.8679 (tp) REVERT: C 322 ASP cc_start: 0.8316 (m-30) cc_final: 0.8089 (m-30) REVERT: C 329 ASN cc_start: 0.8301 (p0) cc_final: 0.8079 (p0) REVERT: C 336 LEU cc_start: 0.9193 (tp) cc_final: 0.8992 (tp) REVERT: C 344 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7816 (ttm110) REVERT: C 347 MET cc_start: 0.8398 (tpp) cc_final: 0.7941 (tpp) REVERT: D 307 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8158 (mm-40) REVERT: D 322 ASP cc_start: 0.8111 (m-30) cc_final: 0.7837 (m-30) REVERT: D 323 ILE cc_start: 0.8766 (mt) cc_final: 0.8449 (mm) REVERT: D 337 SER cc_start: 0.8969 (m) cc_final: 0.8691 (p) REVERT: D 347 MET cc_start: 0.8348 (tpp) cc_final: 0.8106 (tpp) REVERT: D 348 GLN cc_start: 0.8365 (mt0) cc_final: 0.8149 (tt0) REVERT: E 298 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7831 (mm-30) REVERT: E 301 LEU cc_start: 0.8878 (tp) cc_final: 0.8593 (tp) REVERT: E 307 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8496 (mm-40) REVERT: E 347 MET cc_start: 0.8270 (tpp) cc_final: 0.8002 (mpp) REVERT: F 337 SER cc_start: 0.8994 (m) cc_final: 0.8529 (t) REVERT: F 341 SER cc_start: 0.8950 (m) cc_final: 0.8379 (p) REVERT: F 347 MET cc_start: 0.8063 (mmm) cc_final: 0.7619 (tpp) REVERT: F 350 ARG cc_start: 0.8649 (ttm110) cc_final: 0.8439 (ttm110) REVERT: G 292 ARG cc_start: 0.8416 (mtt90) cc_final: 0.8041 (mtt90) REVERT: G 304 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8783 (mm) REVERT: G 318 LEU cc_start: 0.8818 (tp) cc_final: 0.8567 (tp) REVERT: G 322 ASP cc_start: 0.8461 (m-30) cc_final: 0.8017 (m-30) REVERT: G 323 ILE cc_start: 0.8784 (mt) cc_final: 0.8540 (mt) REVERT: G 334 ARG cc_start: 0.8717 (ttm170) cc_final: 0.8244 (ttm170) REVERT: G 337 SER cc_start: 0.8952 (m) cc_final: 0.8485 (t) REVERT: G 341 SER cc_start: 0.8932 (m) cc_final: 0.8642 (p) REVERT: G 347 MET cc_start: 0.8125 (tpp) cc_final: 0.7595 (mpp) REVERT: H 301 LEU cc_start: 0.8747 (tp) cc_final: 0.8346 (tp) REVERT: H 305 LEU cc_start: 0.8922 (mm) cc_final: 0.8634 (mm) REVERT: H 312 PRO cc_start: 0.8786 (Cg_exo) cc_final: 0.8516 (Cg_endo) REVERT: H 314 VAL cc_start: 0.8614 (t) cc_final: 0.8325 (m) REVERT: H 322 ASP cc_start: 0.8387 (m-30) cc_final: 0.7989 (m-30) REVERT: H 334 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.7928 (mtm-85) REVERT: H 347 MET cc_start: 0.8377 (tpp) cc_final: 0.7822 (mpp) REVERT: I 288 LEU cc_start: 0.8693 (mp) cc_final: 0.8057 (mp) REVERT: I 292 ARG cc_start: 0.8595 (mtt90) cc_final: 0.8120 (mtt90) REVERT: I 318 LEU cc_start: 0.8910 (tp) cc_final: 0.8631 (tp) REVERT: I 324 LYS cc_start: 0.8944 (tmtt) cc_final: 0.8542 (tmtt) REVERT: I 348 GLN cc_start: 0.8212 (mt0) cc_final: 0.7939 (mt0) REVERT: J 286 GLU cc_start: 0.8374 (pm20) cc_final: 0.8104 (pm20) REVERT: J 322 ASP cc_start: 0.8197 (m-30) cc_final: 0.7912 (m-30) REVERT: J 337 SER cc_start: 0.8945 (m) cc_final: 0.8564 (p) REVERT: K 292 ARG cc_start: 0.8746 (mtt90) cc_final: 0.8295 (mtt-85) REVERT: K 322 ASP cc_start: 0.8374 (m-30) cc_final: 0.8063 (m-30) REVERT: K 347 MET cc_start: 0.8417 (mmm) cc_final: 0.7843 (tpp) REVERT: K 350 ARG cc_start: 0.8710 (ttm170) cc_final: 0.8421 (ttm170) REVERT: L 318 LEU cc_start: 0.9038 (tp) cc_final: 0.8764 (tp) REVERT: L 337 SER cc_start: 0.8746 (m) cc_final: 0.8515 (m) REVERT: L 347 MET cc_start: 0.8367 (tpp) cc_final: 0.7843 (mpp) REVERT: M 305 LEU cc_start: 0.8902 (mm) cc_final: 0.8563 (mm) REVERT: M 307 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8158 (mm-40) REVERT: M 330 LEU cc_start: 0.8754 (tt) cc_final: 0.8501 (tt) REVERT: M 334 ARG cc_start: 0.8840 (ttm170) cc_final: 0.8505 (ttm170) REVERT: M 337 SER cc_start: 0.8960 (m) cc_final: 0.8718 (m) REVERT: N 305 LEU cc_start: 0.8955 (mm) cc_final: 0.8727 (mm) REVERT: N 307 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8368 (mm-40) REVERT: N 347 MET cc_start: 0.8298 (tpp) cc_final: 0.8057 (mpp) REVERT: N 348 GLN cc_start: 0.8792 (mt0) cc_final: 0.8579 (tt0) REVERT: O 292 ARG cc_start: 0.8771 (mtm-85) cc_final: 0.8346 (mtt-85) REVERT: O 298 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7873 (mm-30) REVERT: O 307 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8650 (mm110) REVERT: O 343 CYS cc_start: 0.8403 (m) cc_final: 0.8159 (m) REVERT: P 290 LEU cc_start: 0.8409 (tt) cc_final: 0.7920 (tt) REVERT: P 294 GLU cc_start: 0.8280 (mp0) cc_final: 0.7611 (mp0) REVERT: P 309 PHE cc_start: 0.8482 (m-80) cc_final: 0.8101 (m-80) REVERT: P 337 SER cc_start: 0.8924 (m) cc_final: 0.8701 (m) REVERT: P 347 MET cc_start: 0.8371 (tpp) cc_final: 0.7925 (mpp) REVERT: Q 339 LEU cc_start: 0.8652 (mm) cc_final: 0.8251 (mm) REVERT: Q 343 CYS cc_start: 0.8533 (m) cc_final: 0.8142 (m) REVERT: Q 344 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8272 (ttm-80) REVERT: R 305 LEU cc_start: 0.9016 (mm) cc_final: 0.8733 (mm) REVERT: R 307 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8288 (mm-40) REVERT: R 337 SER cc_start: 0.8849 (m) cc_final: 0.8483 (p) REVERT: R 350 ARG cc_start: 0.8584 (ttm170) cc_final: 0.8303 (ttm170) REVERT: S 291 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8469 (tp) REVERT: S 298 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7899 (mm-30) REVERT: S 318 LEU cc_start: 0.8817 (tp) cc_final: 0.8565 (tp) REVERT: S 325 SER cc_start: 0.9068 (t) cc_final: 0.8784 (p) REVERT: S 334 ARG cc_start: 0.8454 (ttm-80) cc_final: 0.7934 (mtt90) REVERT: S 337 SER cc_start: 0.8806 (m) cc_final: 0.8527 (m) REVERT: S 341 SER cc_start: 0.8749 (m) cc_final: 0.8314 (p) REVERT: S 350 ARG cc_start: 0.8744 (ttm170) cc_final: 0.8419 (ttm170) REVERT: T 292 ARG cc_start: 0.8444 (mtt90) cc_final: 0.7911 (mtt90) REVERT: T 322 ASP cc_start: 0.8100 (m-30) cc_final: 0.7512 (m-30) REVERT: T 334 ARG cc_start: 0.8318 (ttm170) cc_final: 0.8073 (mmm-85) REVERT: T 344 ARG cc_start: 0.7973 (ttp-110) cc_final: 0.7763 (ttm170) REVERT: T 347 MET cc_start: 0.8473 (tpp) cc_final: 0.7935 (tpp) REVERT: U 288 LEU cc_start: 0.8702 (mp) cc_final: 0.8104 (mp) REVERT: U 292 ARG cc_start: 0.8644 (mtt90) cc_final: 0.8148 (mtt90) REVERT: U 301 LEU cc_start: 0.8807 (tp) cc_final: 0.8271 (tp) REVERT: U 305 LEU cc_start: 0.8766 (mm) cc_final: 0.8483 (mm) REVERT: U 334 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8143 (ttm-80) REVERT: U 347 MET cc_start: 0.8192 (tpp) cc_final: 0.7631 (tpp) REVERT: V 322 ASP cc_start: 0.8173 (m-30) cc_final: 0.7858 (m-30) REVERT: V 334 ARG cc_start: 0.8319 (ttm170) cc_final: 0.7926 (ttm170) REVERT: V 336 LEU cc_start: 0.9039 (tp) cc_final: 0.8767 (tp) REVERT: V 337 SER cc_start: 0.9053 (m) cc_final: 0.8743 (p) REVERT: V 344 ARG cc_start: 0.8039 (ttp-110) cc_final: 0.7680 (ttp-110) REVERT: V 348 GLN cc_start: 0.8631 (mt0) cc_final: 0.8163 (mt0) REVERT: W 286 GLU cc_start: 0.8162 (pm20) cc_final: 0.7918 (pm20) REVERT: W 305 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8710 (mm) REVERT: W 347 MET cc_start: 0.8436 (tpp) cc_final: 0.7764 (mpp) REVERT: X 305 LEU cc_start: 0.9018 (mm) cc_final: 0.8731 (mm) REVERT: X 307 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8335 (mm-40) REVERT: X 322 ASP cc_start: 0.8196 (m-30) cc_final: 0.7833 (m-30) REVERT: X 337 SER cc_start: 0.8782 (m) cc_final: 0.8545 (p) REVERT: X 347 MET cc_start: 0.8318 (tpp) cc_final: 0.7852 (mpp) REVERT: Y 286 GLU cc_start: 0.8415 (pm20) cc_final: 0.8122 (pm20) REVERT: Y 292 ARG cc_start: 0.8699 (mtt90) cc_final: 0.8267 (tpp80) REVERT: Y 301 LEU cc_start: 0.8840 (tp) cc_final: 0.8380 (tp) REVERT: Y 305 LEU cc_start: 0.9094 (mm) cc_final: 0.8789 (mm) REVERT: Z 322 ASP cc_start: 0.8299 (m-30) cc_final: 0.7708 (m-30) REVERT: Z 334 ARG cc_start: 0.8560 (ttm170) cc_final: 0.8052 (ttm-80) REVERT: Z 337 SER cc_start: 0.8755 (m) cc_final: 0.8497 (p) REVERT: Z 338 ARG cc_start: 0.8638 (tpp80) cc_final: 0.8136 (mmm-85) REVERT: Z 344 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7275 (ttm170) REVERT: Z 347 MET cc_start: 0.8259 (tpp) cc_final: 0.7691 (tpp) REVERT: Z 348 GLN cc_start: 0.8403 (mt0) cc_final: 0.8128 (mt0) REVERT: a 338 ARG cc_start: 0.8296 (tpp80) cc_final: 0.7411 (tpp80) REVERT: a 347 MET cc_start: 0.8128 (tpp) cc_final: 0.7307 (tpp) REVERT: c 291 LEU cc_start: 0.9117 (mp) cc_final: 0.8817 (mp) REVERT: c 334 ARG cc_start: 0.8629 (ttm170) cc_final: 0.8402 (ttm170) REVERT: c 347 MET cc_start: 0.8203 (tpp) cc_final: 0.7653 (tpp) outliers start: 68 outliers final: 48 residues processed: 716 average time/residue: 0.1578 time to fit residues: 154.3469 Evaluate side-chains 762 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 711 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain J residue 290 LEU Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 304 LEU Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 323 ILE Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain O residue 290 LEU Chi-restraints excluded: chain O residue 339 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 350 ARG Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain S residue 291 LEU Chi-restraints excluded: chain S residue 339 LEU Chi-restraints excluded: chain T residue 291 LEU Chi-restraints excluded: chain T residue 304 LEU Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 304 LEU Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 304 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 315 LEU Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain Y residue 290 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 339 LEU Chi-restraints excluded: chain a residue 304 LEU Chi-restraints excluded: chain b residue 291 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 11 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN Q 332 GLN S 352 GLN ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.121548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.106244 restraints weight = 25675.581| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.21 r_work: 0.3478 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14840 Z= 0.152 Angle : 0.673 7.473 20076 Z= 0.316 Chirality : 0.040 0.236 2380 Planarity : 0.005 0.047 2660 Dihedral : 4.200 16.683 2100 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 5.16 % Allowed : 20.63 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.20), residues: 1876 helix: 1.95 (0.13), residues: 1736 sheet: None (None), residues: 0 loop : -3.23 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 344 TYR 0.016 0.001 TYR G 284 PHE 0.015 0.001 PHE c 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (14840) covalent geometry : angle 0.67296 / 0.32 (20076) hydrogen bonds : bond 0.02892 / 1.96 ( 1148) hydrogen bonds : angle 3.70505 / 2.59 ( 3444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 726 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 GLU cc_start: 0.8055 (pm20) cc_final: 0.7763 (pm20) REVERT: B 305 LEU cc_start: 0.8909 (mm) cc_final: 0.8609 (mm) REVERT: B 323 ILE cc_start: 0.9045 (mp) cc_final: 0.8837 (mp) REVERT: B 332 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7965 (mm110) REVERT: B 334 ARG cc_start: 0.8619 (ttm170) cc_final: 0.8158 (mmm-85) REVERT: B 348 GLN cc_start: 0.8368 (mt0) cc_final: 0.8158 (mt0) REVERT: C 290 LEU cc_start: 0.8358 (tt) cc_final: 0.7831 (tt) REVERT: C 294 GLU cc_start: 0.8141 (mp0) cc_final: 0.7560 (mp0) REVERT: C 307 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8009 (mm-40) REVERT: C 318 LEU cc_start: 0.8976 (tp) cc_final: 0.8672 (tp) REVERT: C 322 ASP cc_start: 0.8296 (m-30) cc_final: 0.8046 (m-30) REVERT: C 329 ASN cc_start: 0.8355 (p0) cc_final: 0.8142 (p0) REVERT: C 336 LEU cc_start: 0.9187 (tp) cc_final: 0.8969 (tp) REVERT: C 344 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7859 (ttm110) REVERT: C 347 MET cc_start: 0.8360 (tpp) cc_final: 0.8103 (tpp) REVERT: D 307 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8277 (mm-40) REVERT: D 320 ASP cc_start: 0.7897 (t0) cc_final: 0.7602 (t0) REVERT: D 322 ASP cc_start: 0.8086 (m-30) cc_final: 0.7874 (m-30) REVERT: D 323 ILE cc_start: 0.8767 (mt) cc_final: 0.8538 (mt) REVERT: D 337 SER cc_start: 0.9004 (m) cc_final: 0.8708 (p) REVERT: D 347 MET cc_start: 0.8400 (tpp) cc_final: 0.7376 (tpp) REVERT: D 348 GLN cc_start: 0.8377 (mt0) cc_final: 0.8166 (tt0) REVERT: D 350 ARG cc_start: 0.8249 (ttm170) cc_final: 0.7984 (ttm170) REVERT: E 294 GLU cc_start: 0.8208 (mp0) cc_final: 0.7564 (mp0) REVERT: E 298 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7859 (mm-30) REVERT: E 301 LEU cc_start: 0.8889 (tp) cc_final: 0.8641 (tp) REVERT: E 307 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8399 (mm-40) REVERT: E 329 ASN cc_start: 0.8314 (p0) cc_final: 0.8093 (p0) REVERT: E 347 MET cc_start: 0.8302 (tpp) cc_final: 0.8016 (mpp) REVERT: F 322 ASP cc_start: 0.8381 (m-30) cc_final: 0.8148 (m-30) REVERT: F 337 SER cc_start: 0.9014 (m) cc_final: 0.8518 (t) REVERT: F 341 SER cc_start: 0.8925 (m) cc_final: 0.8360 (p) REVERT: F 347 MET cc_start: 0.8038 (mmm) cc_final: 0.7777 (mmm) REVERT: G 292 ARG cc_start: 0.8394 (mtt90) cc_final: 0.7989 (mtt90) REVERT: G 304 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8746 (mm) REVERT: G 318 LEU cc_start: 0.8846 (tp) cc_final: 0.8599 (tp) REVERT: G 322 ASP cc_start: 0.8444 (m-30) cc_final: 0.7870 (m-30) REVERT: G 323 ILE cc_start: 0.8831 (mt) cc_final: 0.8603 (mt) REVERT: G 334 ARG cc_start: 0.8752 (ttm170) cc_final: 0.8114 (mmm-85) REVERT: G 337 SER cc_start: 0.8999 (m) cc_final: 0.8556 (t) REVERT: G 341 SER cc_start: 0.8951 (m) cc_final: 0.8540 (p) REVERT: G 344 ARG cc_start: 0.8191 (ttp-110) cc_final: 0.7605 (mtp-110) REVERT: G 347 MET cc_start: 0.8210 (tpp) cc_final: 0.7682 (mpp) REVERT: H 301 LEU cc_start: 0.8722 (tp) cc_final: 0.8337 (tp) REVERT: H 305 LEU cc_start: 0.8915 (mm) cc_final: 0.8622 (mm) REVERT: H 312 PRO cc_start: 0.8806 (Cg_exo) cc_final: 0.8544 (Cg_endo) REVERT: H 314 VAL cc_start: 0.8602 (t) cc_final: 0.8292 (m) REVERT: H 322 ASP cc_start: 0.8428 (m-30) cc_final: 0.8011 (m-30) REVERT: H 334 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.7728 (mtm-85) REVERT: H 344 ARG cc_start: 0.8018 (ttm170) cc_final: 0.7566 (ttm170) REVERT: H 347 MET cc_start: 0.8436 (tpp) cc_final: 0.7845 (mpp) REVERT: I 288 LEU cc_start: 0.8704 (mp) cc_final: 0.8074 (mp) REVERT: I 292 ARG cc_start: 0.8616 (mtt90) cc_final: 0.8146 (mtt90) REVERT: I 318 LEU cc_start: 0.8891 (tp) cc_final: 0.8653 (tp) REVERT: I 322 ASP cc_start: 0.8247 (m-30) cc_final: 0.6989 (m-30) REVERT: I 334 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.8382 (mmm-85) REVERT: I 348 GLN cc_start: 0.8222 (mt0) cc_final: 0.7981 (mt0) REVERT: J 286 GLU cc_start: 0.8340 (pm20) cc_final: 0.8080 (pm20) REVERT: J 322 ASP cc_start: 0.8198 (m-30) cc_final: 0.7917 (m-30) REVERT: J 334 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8126 (ttm170) REVERT: J 337 SER cc_start: 0.8909 (m) cc_final: 0.8570 (t) REVERT: K 292 ARG cc_start: 0.8732 (mtt90) cc_final: 0.8206 (mtt-85) REVERT: K 315 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8513 (tt) REVERT: K 322 ASP cc_start: 0.8404 (m-30) cc_final: 0.8140 (m-30) REVERT: L 318 LEU cc_start: 0.9006 (tp) cc_final: 0.8756 (tp) REVERT: L 330 LEU cc_start: 0.8730 (tp) cc_final: 0.8430 (tt) REVERT: L 334 ARG cc_start: 0.8800 (ttm170) cc_final: 0.8357 (tpp80) REVERT: L 337 SER cc_start: 0.8766 (m) cc_final: 0.8536 (m) REVERT: L 347 MET cc_start: 0.8324 (tpp) cc_final: 0.7787 (mpp) REVERT: M 294 GLU cc_start: 0.8170 (mp0) cc_final: 0.7639 (mp0) REVERT: M 305 LEU cc_start: 0.8914 (mm) cc_final: 0.8576 (mm) REVERT: M 337 SER cc_start: 0.8963 (m) cc_final: 0.8739 (m) REVERT: N 305 LEU cc_start: 0.8932 (mm) cc_final: 0.8689 (mm) REVERT: N 307 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8242 (mm-40) REVERT: N 347 MET cc_start: 0.8329 (tpp) cc_final: 0.8033 (mpp) REVERT: O 343 CYS cc_start: 0.8589 (m) cc_final: 0.8286 (m) REVERT: O 347 MET cc_start: 0.8323 (tpp) cc_final: 0.7925 (tpp) REVERT: O 350 ARG cc_start: 0.8457 (ttm170) cc_final: 0.8251 (ttm170) REVERT: P 290 LEU cc_start: 0.8403 (tt) cc_final: 0.7975 (tt) REVERT: P 294 GLU cc_start: 0.8269 (mp0) cc_final: 0.7671 (mp0) REVERT: P 337 SER cc_start: 0.8890 (m) cc_final: 0.8685 (m) REVERT: Q 339 LEU cc_start: 0.8657 (mm) cc_final: 0.8282 (mm) REVERT: Q 343 CYS cc_start: 0.8541 (m) cc_final: 0.8123 (m) REVERT: R 305 LEU cc_start: 0.8992 (mm) cc_final: 0.8701 (mm) REVERT: R 307 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8301 (mm-40) REVERT: R 337 SER cc_start: 0.8881 (m) cc_final: 0.8526 (p) REVERT: R 348 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8367 (mt0) REVERT: S 318 LEU cc_start: 0.8819 (tp) cc_final: 0.8536 (tp) REVERT: S 332 GLN cc_start: 0.8577 (mm110) cc_final: 0.8357 (mm110) REVERT: S 334 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.7965 (mtt90) REVERT: S 337 SER cc_start: 0.8841 (m) cc_final: 0.8383 (p) REVERT: S 341 SER cc_start: 0.8755 (m) cc_final: 0.8362 (p) REVERT: S 350 ARG cc_start: 0.8694 (ttm170) cc_final: 0.8411 (ttm170) REVERT: T 292 ARG cc_start: 0.8519 (mtt90) cc_final: 0.8020 (mtt90) REVERT: T 322 ASP cc_start: 0.8084 (m-30) cc_final: 0.7411 (m-30) REVERT: T 334 ARG cc_start: 0.8335 (ttm170) cc_final: 0.8036 (mmm-85) REVERT: T 347 MET cc_start: 0.8438 (tpp) cc_final: 0.7899 (tpp) REVERT: U 288 LEU cc_start: 0.8695 (mp) cc_final: 0.8117 (mp) REVERT: U 292 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8162 (mtt90) REVERT: U 301 LEU cc_start: 0.8795 (tp) cc_final: 0.8258 (tp) REVERT: U 305 LEU cc_start: 0.8796 (mm) cc_final: 0.8498 (mm) REVERT: U 347 MET cc_start: 0.8113 (tpp) cc_final: 0.7646 (tpp) REVERT: V 294 GLU cc_start: 0.8013 (mp0) cc_final: 0.7522 (mp0) REVERT: V 322 ASP cc_start: 0.8130 (m-30) cc_final: 0.7808 (m-30) REVERT: V 334 ARG cc_start: 0.8407 (ttm170) cc_final: 0.7884 (ttm170) REVERT: V 336 LEU cc_start: 0.9003 (tp) cc_final: 0.8735 (tp) REVERT: V 337 SER cc_start: 0.9062 (m) cc_final: 0.8742 (p) REVERT: V 344 ARG cc_start: 0.7994 (ttp-110) cc_final: 0.7611 (ttp-110) REVERT: W 286 GLU cc_start: 0.8151 (pm20) cc_final: 0.7899 (pm20) REVERT: W 305 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8715 (mm) REVERT: W 315 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8324 (tt) REVERT: W 334 ARG cc_start: 0.8607 (ttm170) cc_final: 0.7942 (mmm-85) REVERT: W 347 MET cc_start: 0.8442 (tpp) cc_final: 0.8103 (mmm) REVERT: W 350 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7985 (ttm110) REVERT: X 305 LEU cc_start: 0.8997 (mm) cc_final: 0.8713 (mm) REVERT: X 322 ASP cc_start: 0.8163 (m-30) cc_final: 0.7709 (m-30) REVERT: X 337 SER cc_start: 0.8797 (m) cc_final: 0.8543 (p) REVERT: X 343 CYS cc_start: 0.8677 (m) cc_final: 0.8303 (m) REVERT: X 347 MET cc_start: 0.8382 (tpp) cc_final: 0.7725 (mpp) REVERT: X 350 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7888 (ttm170) REVERT: Y 286 GLU cc_start: 0.8428 (pm20) cc_final: 0.8147 (pm20) REVERT: Y 301 LEU cc_start: 0.8839 (tp) cc_final: 0.8385 (tp) REVERT: Y 304 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8454 (mm) REVERT: Y 305 LEU cc_start: 0.9095 (mm) cc_final: 0.8779 (mm) REVERT: Y 329 ASN cc_start: 0.8364 (p0) cc_final: 0.8098 (p0) REVERT: Z 322 ASP cc_start: 0.8282 (m-30) cc_final: 0.7987 (m-30) REVERT: Z 334 ARG cc_start: 0.8583 (ttm170) cc_final: 0.8053 (ttm-80) REVERT: Z 337 SER cc_start: 0.8740 (m) cc_final: 0.8475 (p) REVERT: Z 338 ARG cc_start: 0.8619 (tpp80) cc_final: 0.8126 (mmm-85) REVERT: Z 347 MET cc_start: 0.8234 (tpp) cc_final: 0.7697 (tpp) REVERT: Z 348 GLN cc_start: 0.8402 (mt0) cc_final: 0.8118 (mt0) REVERT: a 347 MET cc_start: 0.8196 (tpp) cc_final: 0.7357 (tpp) REVERT: b 318 LEU cc_start: 0.9021 (tp) cc_final: 0.8717 (mt) REVERT: b 347 MET cc_start: 0.8187 (tpp) cc_final: 0.7586 (tpp) REVERT: c 334 ARG cc_start: 0.8682 (ttm170) cc_final: 0.8128 (mtt90) outliers start: 78 outliers final: 57 residues processed: 733 average time/residue: 0.1581 time to fit residues: 157.9961 Evaluate side-chains 787 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 723 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 298 GLU Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 315 LEU Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 315 LEU Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 323 ILE Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain O residue 290 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 315 LEU Chi-restraints excluded: chain Q residue 350 ARG Chi-restraints excluded: chain R residue 286 GLU Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 348 GLN Chi-restraints excluded: chain S residue 290 LEU Chi-restraints excluded: chain S residue 317 THR Chi-restraints excluded: chain S residue 339 LEU Chi-restraints excluded: chain T residue 291 LEU Chi-restraints excluded: chain T residue 304 LEU Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 348 GLN Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 304 LEU Chi-restraints excluded: chain W residue 290 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 315 LEU Chi-restraints excluded: chain W residue 350 ARG Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain Y residue 290 LEU Chi-restraints excluded: chain Y residue 304 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 339 LEU Chi-restraints excluded: chain a residue 304 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 0.1980 chunk 110 optimal weight: 0.2980 chunk 158 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 137 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 332 GLN D 332 GLN ** H 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN N 348 GLN Q 332 GLN ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.126784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.111128 restraints weight = 25514.822| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.24 r_work: 0.3491 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14840 Z= 0.123 Angle : 0.673 8.941 20076 Z= 0.309 Chirality : 0.038 0.208 2380 Planarity : 0.005 0.040 2660 Dihedral : 4.024 15.077 2100 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 5.09 % Allowed : 23.15 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.20), residues: 1876 helix: 1.97 (0.13), residues: 1736 sheet: None (None), residues: 0 loop : -3.01 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 344 TYR 0.019 0.001 TYR G 284 PHE 0.016 0.001 PHE Z 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (14840) covalent geometry : angle 0.67302 / 0.31 (20076) hydrogen bonds : bond 0.02612 / 1.77 ( 1148) hydrogen bonds : angle 3.56524 / 2.49 ( 3444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 715 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 GLU cc_start: 0.8053 (pm20) cc_final: 0.7786 (pm20) REVERT: B 291 LEU cc_start: 0.8776 (mp) cc_final: 0.8420 (mp) REVERT: B 305 LEU cc_start: 0.8940 (mm) cc_final: 0.8638 (mm) REVERT: B 332 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7744 (mm110) REVERT: B 334 ARG cc_start: 0.8573 (ttm170) cc_final: 0.8117 (mmm-85) REVERT: C 290 LEU cc_start: 0.8341 (tt) cc_final: 0.7817 (tt) REVERT: C 294 GLU cc_start: 0.8104 (mp0) cc_final: 0.7527 (mp0) REVERT: C 307 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8006 (mm-40) REVERT: C 318 LEU cc_start: 0.8966 (tp) cc_final: 0.8650 (tp) REVERT: C 322 ASP cc_start: 0.8287 (m-30) cc_final: 0.8023 (m-30) REVERT: C 329 ASN cc_start: 0.8364 (p0) cc_final: 0.8153 (p0) REVERT: C 332 GLN cc_start: 0.8252 (mm-40) cc_final: 0.8031 (mm-40) REVERT: C 336 LEU cc_start: 0.9190 (tp) cc_final: 0.8961 (tp) REVERT: C 344 ARG cc_start: 0.8209 (ttm110) cc_final: 0.7873 (ttm110) REVERT: D 291 LEU cc_start: 0.8716 (tp) cc_final: 0.8394 (tp) REVERT: D 307 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8088 (mm-40) REVERT: D 320 ASP cc_start: 0.7888 (t0) cc_final: 0.7493 (t0) REVERT: D 322 ASP cc_start: 0.8057 (m-30) cc_final: 0.7812 (m-30) REVERT: D 323 ILE cc_start: 0.8725 (mt) cc_final: 0.8489 (mt) REVERT: D 337 SER cc_start: 0.8973 (m) cc_final: 0.8684 (p) REVERT: D 347 MET cc_start: 0.8361 (tpp) cc_final: 0.7388 (tpp) REVERT: D 348 GLN cc_start: 0.8366 (mt0) cc_final: 0.8155 (tt0) REVERT: D 350 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7930 (ttm170) REVERT: E 294 GLU cc_start: 0.8218 (mp0) cc_final: 0.7589 (mp0) REVERT: E 298 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7849 (mm-30) REVERT: E 301 LEU cc_start: 0.8872 (tp) cc_final: 0.8650 (tp) REVERT: E 307 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8380 (mm-40) REVERT: E 344 ARG cc_start: 0.8305 (ttp80) cc_final: 0.8090 (ttp-110) REVERT: E 347 MET cc_start: 0.8313 (tpp) cc_final: 0.7985 (mpp) REVERT: F 322 ASP cc_start: 0.8363 (m-30) cc_final: 0.8127 (m-30) REVERT: F 332 GLN cc_start: 0.8729 (mm110) cc_final: 0.8494 (mm110) REVERT: F 337 SER cc_start: 0.8955 (m) cc_final: 0.8502 (p) REVERT: F 341 SER cc_start: 0.8939 (m) cc_final: 0.8366 (p) REVERT: F 347 MET cc_start: 0.7990 (mmm) cc_final: 0.7696 (mmm) REVERT: F 350 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8036 (ttm170) REVERT: G 292 ARG cc_start: 0.8356 (mtt90) cc_final: 0.7966 (mtt90) REVERT: G 304 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8783 (mm) REVERT: G 318 LEU cc_start: 0.8778 (tp) cc_final: 0.8538 (tp) REVERT: G 322 ASP cc_start: 0.8458 (m-30) cc_final: 0.7949 (m-30) REVERT: G 323 ILE cc_start: 0.8812 (mt) cc_final: 0.8573 (mt) REVERT: G 334 ARG cc_start: 0.8767 (ttm170) cc_final: 0.8008 (mtm-85) REVERT: G 337 SER cc_start: 0.8987 (m) cc_final: 0.8531 (t) REVERT: G 341 SER cc_start: 0.8911 (m) cc_final: 0.8527 (p) REVERT: G 344 ARG cc_start: 0.8234 (ttp-110) cc_final: 0.7655 (mtp-110) REVERT: G 347 MET cc_start: 0.8197 (tpp) cc_final: 0.7667 (mpp) REVERT: H 301 LEU cc_start: 0.8690 (tp) cc_final: 0.8313 (tp) REVERT: H 305 LEU cc_start: 0.8881 (mm) cc_final: 0.8575 (mm) REVERT: H 314 VAL cc_start: 0.8546 (t) cc_final: 0.8307 (m) REVERT: H 322 ASP cc_start: 0.8462 (m-30) cc_final: 0.7817 (m-30) REVERT: H 334 ARG cc_start: 0.8393 (mmm-85) cc_final: 0.7782 (mmm-85) REVERT: H 344 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7598 (ttm170) REVERT: H 347 MET cc_start: 0.8469 (tpp) cc_final: 0.7417 (mpp) REVERT: H 350 ARG cc_start: 0.8357 (ttm170) cc_final: 0.7947 (ttm170) REVERT: I 318 LEU cc_start: 0.8933 (tp) cc_final: 0.8680 (tp) REVERT: I 322 ASP cc_start: 0.8254 (m-30) cc_final: 0.7429 (m-30) REVERT: I 334 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8135 (mmm-85) REVERT: I 348 GLN cc_start: 0.8249 (mt0) cc_final: 0.7994 (mt0) REVERT: J 286 GLU cc_start: 0.8300 (pm20) cc_final: 0.8037 (pm20) REVERT: J 322 ASP cc_start: 0.8142 (m-30) cc_final: 0.7908 (m-30) REVERT: J 337 SER cc_start: 0.8896 (m) cc_final: 0.8518 (p) REVERT: K 292 ARG cc_start: 0.8647 (mtt90) cc_final: 0.8162 (mtt-85) REVERT: K 315 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8453 (tt) REVERT: K 322 ASP cc_start: 0.8382 (m-30) cc_final: 0.8073 (m-30) REVERT: K 347 MET cc_start: 0.8237 (mmm) cc_final: 0.7825 (tpp) REVERT: L 318 LEU cc_start: 0.8979 (tp) cc_final: 0.8743 (tp) REVERT: L 347 MET cc_start: 0.8316 (tpp) cc_final: 0.7537 (mpp) REVERT: L 350 ARG cc_start: 0.8579 (ttm170) cc_final: 0.8296 (ttm170) REVERT: M 294 GLU cc_start: 0.8136 (mp0) cc_final: 0.7676 (mp0) REVERT: M 305 LEU cc_start: 0.8908 (mm) cc_final: 0.8560 (mm) REVERT: M 334 ARG cc_start: 0.8771 (ttm170) cc_final: 0.8496 (ttm170) REVERT: M 337 SER cc_start: 0.8910 (m) cc_final: 0.8575 (p) REVERT: N 305 LEU cc_start: 0.8935 (mm) cc_final: 0.8690 (mm) REVERT: N 307 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8210 (mm-40) REVERT: N 347 MET cc_start: 0.8262 (tpp) cc_final: 0.7944 (mpp) REVERT: O 292 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8180 (mtt-85) REVERT: O 343 CYS cc_start: 0.8547 (m) cc_final: 0.8227 (m) REVERT: O 347 MET cc_start: 0.8345 (tpp) cc_final: 0.8026 (tpp) REVERT: P 290 LEU cc_start: 0.8392 (tt) cc_final: 0.7975 (tt) REVERT: P 294 GLU cc_start: 0.8236 (mp0) cc_final: 0.7597 (mp0) REVERT: P 337 SER cc_start: 0.8782 (m) cc_final: 0.8574 (m) REVERT: Q 339 LEU cc_start: 0.8685 (mm) cc_final: 0.8282 (mm) REVERT: Q 343 CYS cc_start: 0.8558 (m) cc_final: 0.8134 (m) REVERT: R 305 LEU cc_start: 0.8996 (mm) cc_final: 0.8741 (mm) REVERT: R 307 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8305 (mm-40) REVERT: R 337 SER cc_start: 0.8825 (m) cc_final: 0.8582 (p) REVERT: S 318 LEU cc_start: 0.8753 (tp) cc_final: 0.8515 (tp) REVERT: S 332 GLN cc_start: 0.8563 (mm110) cc_final: 0.8295 (mm110) REVERT: S 334 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.7867 (mtt90) REVERT: S 337 SER cc_start: 0.8798 (m) cc_final: 0.8334 (p) REVERT: S 341 SER cc_start: 0.8739 (m) cc_final: 0.8361 (p) REVERT: S 350 ARG cc_start: 0.8709 (ttm170) cc_final: 0.8464 (ttm170) REVERT: T 322 ASP cc_start: 0.8023 (m-30) cc_final: 0.7323 (m-30) REVERT: T 332 GLN cc_start: 0.8514 (mm110) cc_final: 0.8048 (mm110) REVERT: T 334 ARG cc_start: 0.8289 (ttm170) cc_final: 0.7844 (mmm-85) REVERT: T 347 MET cc_start: 0.8439 (tpp) cc_final: 0.7937 (tpp) REVERT: U 288 LEU cc_start: 0.8705 (mp) cc_final: 0.8335 (mp) REVERT: U 292 ARG cc_start: 0.8630 (mtt90) cc_final: 0.8195 (mtt90) REVERT: U 301 LEU cc_start: 0.8794 (tp) cc_final: 0.8258 (tp) REVERT: U 305 LEU cc_start: 0.8819 (mm) cc_final: 0.8526 (mm) REVERT: U 334 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8199 (ttm-80) REVERT: V 294 GLU cc_start: 0.8011 (mp0) cc_final: 0.7491 (mp0) REVERT: V 322 ASP cc_start: 0.8143 (m-30) cc_final: 0.7771 (m-30) REVERT: V 334 ARG cc_start: 0.8390 (ttm170) cc_final: 0.7849 (ttm170) REVERT: V 336 LEU cc_start: 0.8981 (tp) cc_final: 0.8742 (tp) REVERT: V 337 SER cc_start: 0.9044 (m) cc_final: 0.8726 (p) REVERT: V 344 ARG cc_start: 0.7952 (ttp-110) cc_final: 0.7555 (ttp-110) REVERT: W 286 GLU cc_start: 0.8166 (pm20) cc_final: 0.7916 (pm20) REVERT: W 305 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8724 (mm) REVERT: W 315 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8315 (tt) REVERT: W 338 ARG cc_start: 0.8421 (tpp80) cc_final: 0.7453 (tpp80) REVERT: W 347 MET cc_start: 0.8412 (tpp) cc_final: 0.8034 (mmm) REVERT: W 348 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: W 350 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7920 (ttm110) REVERT: X 305 LEU cc_start: 0.8995 (mm) cc_final: 0.8697 (mm) REVERT: X 322 ASP cc_start: 0.8188 (m-30) cc_final: 0.7788 (m-30) REVERT: X 337 SER cc_start: 0.8825 (m) cc_final: 0.8588 (p) REVERT: X 343 CYS cc_start: 0.8713 (m) cc_final: 0.8223 (m) REVERT: X 347 MET cc_start: 0.8391 (tpp) cc_final: 0.7687 (mpp) REVERT: X 350 ARG cc_start: 0.8225 (ttm170) cc_final: 0.7869 (ttm170) REVERT: Y 286 GLU cc_start: 0.8423 (pm20) cc_final: 0.8144 (pm20) REVERT: Y 292 ARG cc_start: 0.8641 (mtt90) cc_final: 0.8367 (mtt90) REVERT: Y 301 LEU cc_start: 0.8814 (tp) cc_final: 0.8377 (tp) REVERT: Y 304 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8450 (mm) REVERT: Y 305 LEU cc_start: 0.9086 (mm) cc_final: 0.8765 (mm) REVERT: Y 329 ASN cc_start: 0.8389 (p0) cc_final: 0.8112 (p0) REVERT: Z 329 ASN cc_start: 0.7127 (t0) cc_final: 0.6924 (t0) REVERT: Z 334 ARG cc_start: 0.8570 (ttm170) cc_final: 0.7956 (ttm-80) REVERT: Z 337 SER cc_start: 0.8702 (m) cc_final: 0.8419 (p) REVERT: Z 338 ARG cc_start: 0.8604 (tpp80) cc_final: 0.8088 (mmm-85) REVERT: Z 348 GLN cc_start: 0.8375 (mt0) cc_final: 0.8004 (mt0) REVERT: a 347 MET cc_start: 0.8219 (tpp) cc_final: 0.7417 (tpp) REVERT: b 318 LEU cc_start: 0.9019 (tp) cc_final: 0.8394 (mt) REVERT: b 347 MET cc_start: 0.8171 (tpp) cc_final: 0.7503 (tpp) REVERT: c 334 ARG cc_start: 0.8653 (ttm170) cc_final: 0.8065 (mtt90) REVERT: c 347 MET cc_start: 0.8269 (tpp) cc_final: 0.7631 (tpp) outliers start: 77 outliers final: 54 residues processed: 721 average time/residue: 0.1553 time to fit residues: 153.1136 Evaluate side-chains 775 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 714 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 290 LEU Chi-restraints excluded: chain J residue 298 GLU Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 315 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 315 LEU Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 315 LEU Chi-restraints excluded: chain N residue 323 ILE Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 315 LEU Chi-restraints excluded: chain Q residue 350 ARG Chi-restraints excluded: chain R residue 286 GLU Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain S residue 290 LEU Chi-restraints excluded: chain S residue 339 LEU Chi-restraints excluded: chain T residue 291 LEU Chi-restraints excluded: chain T residue 304 LEU Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 315 LEU Chi-restraints excluded: chain U residue 339 LEU Chi-restraints excluded: chain V residue 304 LEU Chi-restraints excluded: chain W residue 304 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 315 LEU Chi-restraints excluded: chain W residue 348 GLN Chi-restraints excluded: chain W residue 350 ARG Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain Y residue 291 LEU Chi-restraints excluded: chain Y residue 304 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 317 THR Chi-restraints excluded: chain a residue 304 LEU Chi-restraints excluded: chain b residue 291 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 114 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 146 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN Q 332 GLN R 352 GLN T 307 GLN ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 352 GLN U 332 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.127318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.113108 restraints weight = 25610.161| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.31 r_work: 0.3485 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14840 Z= 0.144 Angle : 0.677 9.457 20076 Z= 0.314 Chirality : 0.039 0.221 2380 Planarity : 0.005 0.040 2660 Dihedral : 4.049 15.830 2100 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 5.03 % Allowed : 24.14 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.20), residues: 1876 helix: 1.82 (0.13), residues: 1764 sheet: None (None), residues: 0 loop : -6.03 (0.16), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 344 TYR 0.019 0.001 TYR G 284 PHE 0.016 0.001 PHE Z 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (14840) covalent geometry : angle 0.67660 / 0.31 (20076) hydrogen bonds : bond 0.02786 / 1.89 ( 1148) hydrogen bonds : angle 3.58523 / 2.51 ( 3444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 716 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 LEU cc_start: 0.8777 (mp) cc_final: 0.8413 (mp) REVERT: B 305 LEU cc_start: 0.8963 (mm) cc_final: 0.8677 (mm) REVERT: B 334 ARG cc_start: 0.8635 (ttm170) cc_final: 0.8178 (mmm-85) REVERT: B 348 GLN cc_start: 0.8370 (mt0) cc_final: 0.8168 (mt0) REVERT: C 290 LEU cc_start: 0.8333 (tt) cc_final: 0.7797 (tt) REVERT: C 294 GLU cc_start: 0.8161 (mp0) cc_final: 0.7576 (mp0) REVERT: C 307 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8068 (mm-40) REVERT: C 318 LEU cc_start: 0.8968 (tp) cc_final: 0.8636 (tp) REVERT: C 322 ASP cc_start: 0.8300 (m-30) cc_final: 0.7989 (m-30) REVERT: C 329 ASN cc_start: 0.8385 (p0) cc_final: 0.8171 (p0) REVERT: C 336 LEU cc_start: 0.9205 (tp) cc_final: 0.8987 (tp) REVERT: C 344 ARG cc_start: 0.8273 (ttm110) cc_final: 0.7919 (ttm110) REVERT: C 347 MET cc_start: 0.8400 (tpp) cc_final: 0.8155 (tpp) REVERT: D 307 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8285 (mm-40) REVERT: D 320 ASP cc_start: 0.8043 (t0) cc_final: 0.7710 (t0) REVERT: D 322 ASP cc_start: 0.8130 (m-30) cc_final: 0.7839 (m-30) REVERT: D 323 ILE cc_start: 0.8759 (mt) cc_final: 0.8538 (mt) REVERT: D 337 SER cc_start: 0.8956 (m) cc_final: 0.8682 (p) REVERT: D 347 MET cc_start: 0.8352 (tpp) cc_final: 0.7407 (tpp) REVERT: D 348 GLN cc_start: 0.8364 (mt0) cc_final: 0.8160 (tt0) REVERT: D 350 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7956 (ttm170) REVERT: E 294 GLU cc_start: 0.8262 (mp0) cc_final: 0.7558 (mp0) REVERT: E 298 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7872 (mm-30) REVERT: E 301 LEU cc_start: 0.8883 (tp) cc_final: 0.8670 (tp) REVERT: E 307 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8380 (mm-40) REVERT: E 329 ASN cc_start: 0.8277 (p0) cc_final: 0.8026 (p0) REVERT: E 347 MET cc_start: 0.8342 (tpp) cc_final: 0.8022 (mpp) REVERT: F 337 SER cc_start: 0.8998 (m) cc_final: 0.8533 (t) REVERT: F 341 SER cc_start: 0.8917 (m) cc_final: 0.8387 (p) REVERT: G 286 GLU cc_start: 0.8341 (pm20) cc_final: 0.8127 (pm20) REVERT: G 288 LEU cc_start: 0.8934 (mp) cc_final: 0.8666 (mp) REVERT: G 292 ARG cc_start: 0.8407 (mtt90) cc_final: 0.8028 (mtt90) REVERT: G 304 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8689 (mm) REVERT: G 318 LEU cc_start: 0.8801 (tp) cc_final: 0.8549 (tp) REVERT: G 322 ASP cc_start: 0.8434 (m-30) cc_final: 0.7895 (m-30) REVERT: G 323 ILE cc_start: 0.8831 (mt) cc_final: 0.8614 (mt) REVERT: G 332 GLN cc_start: 0.8464 (mm110) cc_final: 0.8122 (mm110) REVERT: G 334 ARG cc_start: 0.8797 (ttm170) cc_final: 0.8052 (mmm-85) REVERT: G 337 SER cc_start: 0.8997 (m) cc_final: 0.8563 (t) REVERT: G 341 SER cc_start: 0.8939 (m) cc_final: 0.8527 (p) REVERT: G 344 ARG cc_start: 0.8268 (ttp-110) cc_final: 0.7619 (mtp-110) REVERT: G 347 MET cc_start: 0.8247 (tpp) cc_final: 0.7698 (mpp) REVERT: H 301 LEU cc_start: 0.8738 (tp) cc_final: 0.8377 (tp) REVERT: H 305 LEU cc_start: 0.8905 (mm) cc_final: 0.8599 (mm) REVERT: H 314 VAL cc_start: 0.8580 (t) cc_final: 0.8270 (m) REVERT: H 322 ASP cc_start: 0.8485 (m-30) cc_final: 0.7977 (m-30) REVERT: H 334 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.7687 (mmm-85) REVERT: H 344 ARG cc_start: 0.8020 (ttm170) cc_final: 0.7555 (ttm170) REVERT: H 347 MET cc_start: 0.8524 (tpp) cc_final: 0.7484 (mpp) REVERT: H 350 ARG cc_start: 0.8404 (ttm170) cc_final: 0.8015 (ttm170) REVERT: I 292 ARG cc_start: 0.8586 (mtt90) cc_final: 0.8090 (mtt90) REVERT: I 318 LEU cc_start: 0.8900 (tp) cc_final: 0.8657 (tp) REVERT: I 322 ASP cc_start: 0.8284 (m-30) cc_final: 0.7326 (m-30) REVERT: I 326 VAL cc_start: 0.8825 (t) cc_final: 0.8620 (p) REVERT: I 348 GLN cc_start: 0.8293 (mt0) cc_final: 0.8049 (mt0) REVERT: J 286 GLU cc_start: 0.8274 (pm20) cc_final: 0.8029 (pm20) REVERT: J 334 ARG cc_start: 0.8428 (ttm170) cc_final: 0.7918 (ttm170) REVERT: J 337 SER cc_start: 0.8888 (m) cc_final: 0.8529 (p) REVERT: K 292 ARG cc_start: 0.8671 (mtt90) cc_final: 0.8086 (mtt-85) REVERT: K 315 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8482 (tt) REVERT: K 322 ASP cc_start: 0.8420 (m-30) cc_final: 0.8105 (m-30) REVERT: K 347 MET cc_start: 0.8286 (mmm) cc_final: 0.7853 (tpp) REVERT: L 318 LEU cc_start: 0.8977 (tp) cc_final: 0.8723 (tp) REVERT: L 330 LEU cc_start: 0.8789 (tp) cc_final: 0.8379 (tt) REVERT: L 334 ARG cc_start: 0.8758 (ttm170) cc_final: 0.8406 (ttm170) REVERT: L 347 MET cc_start: 0.8334 (tpp) cc_final: 0.7399 (mpp) REVERT: L 350 ARG cc_start: 0.8557 (ttm170) cc_final: 0.8264 (ttm170) REVERT: M 294 GLU cc_start: 0.8116 (mp0) cc_final: 0.7663 (mp0) REVERT: M 305 LEU cc_start: 0.8879 (mm) cc_final: 0.8529 (mm) REVERT: M 334 ARG cc_start: 0.8847 (ttm170) cc_final: 0.8544 (ttm170) REVERT: M 337 SER cc_start: 0.8947 (m) cc_final: 0.8591 (p) REVERT: N 305 LEU cc_start: 0.8938 (mm) cc_final: 0.8696 (mm) REVERT: N 307 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8139 (mm-40) REVERT: N 347 MET cc_start: 0.8335 (tpp) cc_final: 0.7970 (mpp) REVERT: O 343 CYS cc_start: 0.8681 (m) cc_final: 0.8379 (m) REVERT: O 347 MET cc_start: 0.8537 (tpp) cc_final: 0.8180 (tpp) REVERT: P 287 PHE cc_start: 0.8459 (t80) cc_final: 0.8191 (t80) REVERT: P 290 LEU cc_start: 0.8391 (tt) cc_final: 0.8013 (tt) REVERT: P 294 GLU cc_start: 0.8202 (mp0) cc_final: 0.7557 (mp0) REVERT: P 337 SER cc_start: 0.8743 (m) cc_final: 0.8319 (p) REVERT: Q 339 LEU cc_start: 0.8727 (mm) cc_final: 0.8348 (mm) REVERT: Q 343 CYS cc_start: 0.8621 (m) cc_final: 0.8225 (m) REVERT: R 305 LEU cc_start: 0.8948 (mm) cc_final: 0.8683 (mm) REVERT: R 307 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8277 (mm-40) REVERT: R 337 SER cc_start: 0.8889 (m) cc_final: 0.8440 (p) REVERT: R 348 GLN cc_start: 0.8297 (mt0) cc_final: 0.8027 (tt0) REVERT: S 318 LEU cc_start: 0.8756 (tp) cc_final: 0.8515 (tp) REVERT: S 334 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.7956 (mtt90) REVERT: S 337 SER cc_start: 0.8798 (m) cc_final: 0.8390 (p) REVERT: S 341 SER cc_start: 0.8709 (m) cc_final: 0.8326 (p) REVERT: S 350 ARG cc_start: 0.8741 (ttm170) cc_final: 0.8531 (ttm170) REVERT: T 334 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7930 (mmm-85) REVERT: T 347 MET cc_start: 0.8424 (tpp) cc_final: 0.7932 (tpp) REVERT: U 301 LEU cc_start: 0.8771 (tp) cc_final: 0.8248 (tp) REVERT: U 305 LEU cc_start: 0.8831 (mm) cc_final: 0.8534 (mm) REVERT: U 334 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8182 (ttm-80) REVERT: V 294 GLU cc_start: 0.8017 (mp0) cc_final: 0.7578 (mp0) REVERT: V 322 ASP cc_start: 0.8138 (m-30) cc_final: 0.7785 (m-30) REVERT: V 334 ARG cc_start: 0.8404 (ttm170) cc_final: 0.7817 (ttm170) REVERT: V 336 LEU cc_start: 0.9066 (tp) cc_final: 0.8845 (tp) REVERT: V 337 SER cc_start: 0.9110 (m) cc_final: 0.8776 (p) REVERT: V 344 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7613 (ttp-110) REVERT: W 286 GLU cc_start: 0.8139 (pm20) cc_final: 0.7889 (pm20) REVERT: W 305 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8734 (mm) REVERT: W 315 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8370 (tt) REVERT: W 334 ARG cc_start: 0.8584 (ttm170) cc_final: 0.7898 (mmm-85) REVERT: W 338 ARG cc_start: 0.8502 (tpp80) cc_final: 0.7532 (tpp80) REVERT: W 347 MET cc_start: 0.8414 (tpp) cc_final: 0.8069 (mmm) REVERT: W 350 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7920 (ttm110) REVERT: X 305 LEU cc_start: 0.9007 (mm) cc_final: 0.8695 (mm) REVERT: X 307 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8148 (mm-40) REVERT: X 322 ASP cc_start: 0.8173 (m-30) cc_final: 0.7692 (m-30) REVERT: X 337 SER cc_start: 0.8788 (m) cc_final: 0.8565 (p) REVERT: X 343 CYS cc_start: 0.8729 (m) cc_final: 0.8282 (m) REVERT: X 347 MET cc_start: 0.8462 (tpp) cc_final: 0.7783 (mpp) REVERT: X 350 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7829 (ttm170) REVERT: Y 286 GLU cc_start: 0.8409 (pm20) cc_final: 0.8135 (pm20) REVERT: Y 292 ARG cc_start: 0.8647 (mtt90) cc_final: 0.8359 (mtt90) REVERT: Y 301 LEU cc_start: 0.8803 (tp) cc_final: 0.8381 (tp) REVERT: Y 304 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8424 (mm) REVERT: Y 305 LEU cc_start: 0.9073 (mm) cc_final: 0.8769 (mm) REVERT: Y 323 ILE cc_start: 0.8500 (mp) cc_final: 0.8250 (mp) REVERT: Y 329 ASN cc_start: 0.8396 (p0) cc_final: 0.8096 (p0) REVERT: Z 304 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7914 (mm) REVERT: Z 329 ASN cc_start: 0.7144 (t0) cc_final: 0.6910 (t0) REVERT: Z 334 ARG cc_start: 0.8578 (ttm170) cc_final: 0.7967 (ttm-80) REVERT: Z 337 SER cc_start: 0.8736 (m) cc_final: 0.8445 (p) REVERT: Z 338 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8150 (mmm-85) REVERT: Z 348 GLN cc_start: 0.8405 (mt0) cc_final: 0.8037 (mt0) REVERT: a 347 MET cc_start: 0.8227 (tpp) cc_final: 0.7448 (tpp) REVERT: b 318 LEU cc_start: 0.9008 (tp) cc_final: 0.8740 (mt) REVERT: b 347 MET cc_start: 0.8229 (tpp) cc_final: 0.7563 (tpp) REVERT: c 304 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8096 (mm) REVERT: c 334 ARG cc_start: 0.8695 (ttm170) cc_final: 0.8127 (mtt90) REVERT: c 347 MET cc_start: 0.8243 (tpp) cc_final: 0.7651 (tpp) outliers start: 76 outliers final: 56 residues processed: 720 average time/residue: 0.1482 time to fit residues: 144.9105 Evaluate side-chains 780 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 716 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 298 GLU Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 315 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 304 LEU Chi-restraints excluded: chain L residue 315 LEU Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 315 LEU Chi-restraints excluded: chain N residue 323 ILE Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain O residue 304 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain Q residue 290 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 315 LEU Chi-restraints excluded: chain Q residue 350 ARG Chi-restraints excluded: chain R residue 286 GLU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain S residue 290 LEU Chi-restraints excluded: chain S residue 317 THR Chi-restraints excluded: chain S residue 339 LEU Chi-restraints excluded: chain T residue 291 LEU Chi-restraints excluded: chain T residue 304 LEU Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 315 LEU Chi-restraints excluded: chain V residue 304 LEU Chi-restraints excluded: chain W residue 304 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 315 LEU Chi-restraints excluded: chain W residue 350 ARG Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain Y residue 291 LEU Chi-restraints excluded: chain Y residue 304 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 317 THR Chi-restraints excluded: chain Z residue 304 LEU Chi-restraints excluded: chain a residue 304 LEU Chi-restraints excluded: chain b residue 291 LEU Chi-restraints excluded: chain c residue 304 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 133 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 332 GLN ** H 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN Q 332 GLN ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.126691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.110616 restraints weight = 25566.905| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.24 r_work: 0.3469 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14840 Z= 0.142 Angle : 0.701 10.028 20076 Z= 0.321 Chirality : 0.040 0.235 2380 Planarity : 0.005 0.039 2660 Dihedral : 4.025 15.756 2100 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 5.49 % Allowed : 24.74 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.20), residues: 1876 helix: 1.76 (0.12), residues: 1764 sheet: None (None), residues: 0 loop : -6.06 (0.17), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 344 TYR 0.020 0.001 TYR G 284 PHE 0.017 0.001 PHE Z 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14840) covalent geometry : angle 0.70066 / 0.32 (20076) hydrogen bonds : bond 0.02775 / 1.88 ( 1148) hydrogen bonds : angle 3.59962 / 2.52 ( 3444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 714 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 LEU cc_start: 0.8767 (mp) cc_final: 0.8412 (mp) REVERT: B 294 GLU cc_start: 0.7935 (mp0) cc_final: 0.7726 (mp0) REVERT: B 298 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8241 (mm-30) REVERT: B 305 LEU cc_start: 0.8969 (mm) cc_final: 0.8701 (mm) REVERT: B 329 ASN cc_start: 0.8121 (p0) cc_final: 0.7837 (p0) REVERT: B 332 GLN cc_start: 0.8300 (mm110) cc_final: 0.7891 (mm110) REVERT: B 334 ARG cc_start: 0.8563 (ttm170) cc_final: 0.7957 (mmm-85) REVERT: C 290 LEU cc_start: 0.8326 (tt) cc_final: 0.7765 (tt) REVERT: C 294 GLU cc_start: 0.8129 (mp0) cc_final: 0.7554 (mp0) REVERT: C 307 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8117 (mm-40) REVERT: C 318 LEU cc_start: 0.8982 (tp) cc_final: 0.8618 (tp) REVERT: C 322 ASP cc_start: 0.8258 (m-30) cc_final: 0.7946 (m-30) REVERT: C 329 ASN cc_start: 0.8379 (p0) cc_final: 0.8141 (p0) REVERT: C 332 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7911 (mm-40) REVERT: C 336 LEU cc_start: 0.9193 (tp) cc_final: 0.8971 (tp) REVERT: C 344 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7813 (ttm110) REVERT: C 347 MET cc_start: 0.8369 (tpp) cc_final: 0.8154 (tpp) REVERT: D 307 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8112 (mm-40) REVERT: D 322 ASP cc_start: 0.8021 (m-30) cc_final: 0.7632 (m-30) REVERT: D 323 ILE cc_start: 0.8745 (mt) cc_final: 0.8526 (mt) REVERT: D 337 SER cc_start: 0.9000 (m) cc_final: 0.8705 (p) REVERT: D 347 MET cc_start: 0.8370 (tpp) cc_final: 0.7352 (tpp) REVERT: D 350 ARG cc_start: 0.8212 (ttm170) cc_final: 0.7947 (ttm170) REVERT: E 294 GLU cc_start: 0.8108 (mp0) cc_final: 0.7723 (mp0) REVERT: E 298 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7843 (mm-30) REVERT: E 329 ASN cc_start: 0.8324 (p0) cc_final: 0.8080 (p0) REVERT: E 347 MET cc_start: 0.8340 (tpp) cc_final: 0.8016 (mpp) REVERT: F 315 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8416 (tt) REVERT: F 334 ARG cc_start: 0.8754 (ttm170) cc_final: 0.8543 (ttm170) REVERT: F 337 SER cc_start: 0.8993 (m) cc_final: 0.8488 (t) REVERT: F 341 SER cc_start: 0.8894 (m) cc_final: 0.8355 (p) REVERT: G 286 GLU cc_start: 0.8352 (pm20) cc_final: 0.8112 (pm20) REVERT: G 288 LEU cc_start: 0.8927 (mp) cc_final: 0.8627 (mp) REVERT: G 292 ARG cc_start: 0.8350 (mtt90) cc_final: 0.7956 (mtt90) REVERT: G 294 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: G 318 LEU cc_start: 0.8779 (tp) cc_final: 0.8526 (tp) REVERT: G 322 ASP cc_start: 0.8421 (m-30) cc_final: 0.7830 (m-30) REVERT: G 323 ILE cc_start: 0.8831 (mt) cc_final: 0.8618 (mt) REVERT: G 332 GLN cc_start: 0.8459 (mm110) cc_final: 0.8119 (mm110) REVERT: G 334 ARG cc_start: 0.8782 (ttm170) cc_final: 0.7731 (mtt180) REVERT: G 337 SER cc_start: 0.9025 (m) cc_final: 0.8583 (t) REVERT: G 341 SER cc_start: 0.8926 (m) cc_final: 0.8533 (p) REVERT: G 344 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7518 (mtp-110) REVERT: G 347 MET cc_start: 0.8236 (tpp) cc_final: 0.7699 (mpp) REVERT: H 301 LEU cc_start: 0.8704 (tp) cc_final: 0.8397 (tp) REVERT: H 305 LEU cc_start: 0.8934 (mm) cc_final: 0.8660 (mm) REVERT: H 312 PRO cc_start: 0.8795 (Cg_exo) cc_final: 0.8524 (Cg_endo) REVERT: H 314 VAL cc_start: 0.8545 (t) cc_final: 0.8295 (m) REVERT: H 322 ASP cc_start: 0.8444 (m-30) cc_final: 0.7684 (m-30) REVERT: H 334 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7592 (mmm-85) REVERT: H 344 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7380 (ttm170) REVERT: H 347 MET cc_start: 0.8503 (tpp) cc_final: 0.7465 (mpp) REVERT: H 350 ARG cc_start: 0.8427 (ttm170) cc_final: 0.8037 (ttm170) REVERT: I 318 LEU cc_start: 0.8893 (tp) cc_final: 0.8636 (tp) REVERT: I 322 ASP cc_start: 0.8271 (m-30) cc_final: 0.7097 (m-30) REVERT: I 334 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8303 (mmm-85) REVERT: I 348 GLN cc_start: 0.8286 (mt0) cc_final: 0.8034 (mt0) REVERT: J 286 GLU cc_start: 0.8271 (pm20) cc_final: 0.8040 (pm20) REVERT: J 334 ARG cc_start: 0.8418 (ttm170) cc_final: 0.7904 (ttm170) REVERT: J 337 SER cc_start: 0.8902 (m) cc_final: 0.8552 (p) REVERT: K 292 ARG cc_start: 0.8638 (mtt90) cc_final: 0.8135 (mtt-85) REVERT: K 315 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8484 (tt) REVERT: K 322 ASP cc_start: 0.8402 (m-30) cc_final: 0.8081 (m-30) REVERT: K 347 MET cc_start: 0.8288 (mmm) cc_final: 0.7854 (tpp) REVERT: L 318 LEU cc_start: 0.8997 (tp) cc_final: 0.8760 (tp) REVERT: L 334 ARG cc_start: 0.8774 (ttm170) cc_final: 0.8461 (ttm170) REVERT: L 347 MET cc_start: 0.8340 (tpp) cc_final: 0.7439 (mpp) REVERT: L 350 ARG cc_start: 0.8573 (ttm170) cc_final: 0.8264 (ttm170) REVERT: M 292 ARG cc_start: 0.8509 (mtt90) cc_final: 0.8048 (mtt-85) REVERT: M 294 GLU cc_start: 0.8120 (mp0) cc_final: 0.7702 (mp0) REVERT: M 305 LEU cc_start: 0.8883 (mm) cc_final: 0.8536 (mm) REVERT: M 337 SER cc_start: 0.8943 (m) cc_final: 0.8610 (p) REVERT: N 305 LEU cc_start: 0.8949 (mm) cc_final: 0.8710 (mm) REVERT: N 307 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8063 (mm-40) REVERT: N 347 MET cc_start: 0.8277 (tpp) cc_final: 0.7932 (mpp) REVERT: O 292 ARG cc_start: 0.8735 (mtm-85) cc_final: 0.8379 (mtt-85) REVERT: O 343 CYS cc_start: 0.8690 (m) cc_final: 0.8405 (m) REVERT: O 347 MET cc_start: 0.8629 (tpp) cc_final: 0.8317 (tpp) REVERT: P 287 PHE cc_start: 0.8442 (t80) cc_final: 0.8164 (t80) REVERT: P 290 LEU cc_start: 0.8351 (tt) cc_final: 0.7984 (tt) REVERT: P 294 GLU cc_start: 0.8208 (mp0) cc_final: 0.7549 (mp0) REVERT: P 337 SER cc_start: 0.8748 (m) cc_final: 0.8324 (p) REVERT: Q 334 ARG cc_start: 0.8690 (ttm170) cc_final: 0.7689 (mtm180) REVERT: Q 339 LEU cc_start: 0.8718 (mm) cc_final: 0.8335 (mm) REVERT: Q 343 CYS cc_start: 0.8615 (m) cc_final: 0.8231 (m) REVERT: R 294 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: R 305 LEU cc_start: 0.8990 (mm) cc_final: 0.8722 (mm) REVERT: R 307 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8291 (mm-40) REVERT: R 337 SER cc_start: 0.8860 (m) cc_final: 0.8532 (p) REVERT: R 348 GLN cc_start: 0.8305 (mt0) cc_final: 0.8016 (tt0) REVERT: R 350 ARG cc_start: 0.8615 (ttm170) cc_final: 0.8390 (ttm170) REVERT: S 292 ARG cc_start: 0.8582 (mtt90) cc_final: 0.8370 (ptp-170) REVERT: S 318 LEU cc_start: 0.8764 (tp) cc_final: 0.8521 (tp) REVERT: S 334 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.7982 (mtt90) REVERT: S 337 SER cc_start: 0.8830 (m) cc_final: 0.8423 (p) REVERT: S 341 SER cc_start: 0.8743 (m) cc_final: 0.8371 (p) REVERT: S 350 ARG cc_start: 0.8698 (ttm170) cc_final: 0.8473 (ttm170) REVERT: T 324 LYS cc_start: 0.8911 (tmtt) cc_final: 0.8553 (tmtt) REVERT: T 334 ARG cc_start: 0.8249 (ttm170) cc_final: 0.7897 (mmm-85) REVERT: T 347 MET cc_start: 0.8462 (tpp) cc_final: 0.7990 (tpp) REVERT: U 301 LEU cc_start: 0.8764 (tp) cc_final: 0.8222 (tp) REVERT: U 305 LEU cc_start: 0.8817 (mm) cc_final: 0.8515 (mm) REVERT: U 334 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8266 (ttm-80) REVERT: U 347 MET cc_start: 0.8261 (tpp) cc_final: 0.8054 (tpp) REVERT: V 322 ASP cc_start: 0.8122 (m-30) cc_final: 0.7756 (m-30) REVERT: V 334 ARG cc_start: 0.8352 (ttm170) cc_final: 0.7823 (ttm170) REVERT: V 336 LEU cc_start: 0.9010 (tp) cc_final: 0.8786 (tp) REVERT: V 337 SER cc_start: 0.9070 (m) cc_final: 0.8743 (p) REVERT: V 344 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7563 (ttp-110) REVERT: W 286 GLU cc_start: 0.8196 (pm20) cc_final: 0.7929 (pm20) REVERT: W 305 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8762 (mm) REVERT: W 315 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8392 (tt) REVERT: W 338 ARG cc_start: 0.8449 (tpp80) cc_final: 0.7522 (tpp80) REVERT: W 347 MET cc_start: 0.8367 (tpp) cc_final: 0.7782 (mpp) REVERT: X 305 LEU cc_start: 0.9001 (mm) cc_final: 0.8686 (mm) REVERT: X 307 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8039 (mm-40) REVERT: X 322 ASP cc_start: 0.8142 (m-30) cc_final: 0.7750 (m-30) REVERT: X 337 SER cc_start: 0.8836 (m) cc_final: 0.8619 (p) REVERT: X 347 MET cc_start: 0.8361 (tpp) cc_final: 0.7671 (mpp) REVERT: X 350 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7889 (ttm170) REVERT: Y 286 GLU cc_start: 0.8386 (pm20) cc_final: 0.8104 (pm20) REVERT: Y 292 ARG cc_start: 0.8607 (mtt90) cc_final: 0.8327 (mtt90) REVERT: Y 301 LEU cc_start: 0.8815 (tp) cc_final: 0.8388 (tp) REVERT: Y 304 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8492 (mm) REVERT: Y 305 LEU cc_start: 0.9087 (mm) cc_final: 0.8785 (mm) REVERT: Y 323 ILE cc_start: 0.8505 (mp) cc_final: 0.8236 (mp) REVERT: Y 329 ASN cc_start: 0.8442 (p0) cc_final: 0.8171 (p0) REVERT: Z 304 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7891 (mm) REVERT: Z 329 ASN cc_start: 0.7256 (t0) cc_final: 0.6983 (t0) REVERT: Z 334 ARG cc_start: 0.8647 (ttm170) cc_final: 0.8028 (ttm-80) REVERT: Z 337 SER cc_start: 0.8749 (m) cc_final: 0.8467 (p) REVERT: Z 338 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8139 (mmm-85) REVERT: Z 348 GLN cc_start: 0.8450 (mt0) cc_final: 0.8067 (mt0) REVERT: a 344 ARG cc_start: 0.7571 (ttp-110) cc_final: 0.7115 (ttp80) REVERT: a 347 MET cc_start: 0.8224 (tpp) cc_final: 0.7451 (tpp) REVERT: b 318 LEU cc_start: 0.8993 (tp) cc_final: 0.8441 (mt) REVERT: b 347 MET cc_start: 0.8190 (tpp) cc_final: 0.7546 (tpp) REVERT: c 304 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8093 (mm) REVERT: c 334 ARG cc_start: 0.8686 (ttm170) cc_final: 0.8161 (mtt90) REVERT: c 347 MET cc_start: 0.8353 (tpp) cc_final: 0.7768 (tpp) outliers start: 83 outliers final: 60 residues processed: 722 average time/residue: 0.1463 time to fit residues: 143.7277 Evaluate side-chains 785 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 715 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 298 GLU Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 315 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 304 LEU Chi-restraints excluded: chain L residue 315 LEU Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 315 LEU Chi-restraints excluded: chain N residue 323 ILE Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain O residue 304 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain Q residue 290 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 315 LEU Chi-restraints excluded: chain Q residue 350 ARG Chi-restraints excluded: chain R residue 286 GLU Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain S residue 290 LEU Chi-restraints excluded: chain S residue 304 LEU Chi-restraints excluded: chain S residue 317 THR Chi-restraints excluded: chain S residue 339 LEU Chi-restraints excluded: chain T residue 291 LEU Chi-restraints excluded: chain T residue 304 LEU Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 304 LEU Chi-restraints excluded: chain V residue 304 LEU Chi-restraints excluded: chain V residue 348 GLN Chi-restraints excluded: chain W residue 304 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 315 LEU Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain Y residue 291 LEU Chi-restraints excluded: chain Y residue 304 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 317 THR Chi-restraints excluded: chain Z residue 304 LEU Chi-restraints excluded: chain a residue 304 LEU Chi-restraints excluded: chain b residue 291 LEU Chi-restraints excluded: chain c residue 304 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 104 optimal weight: 0.0170 chunk 100 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 332 GLN D 348 GLN ** H 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 348 GLN M 332 GLN ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 348 GLN W 348 GLN X 348 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.126697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.112265 restraints weight = 25876.045| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.25 r_work: 0.3492 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14840 Z= 0.140 Angle : 0.720 10.405 20076 Z= 0.328 Chirality : 0.040 0.263 2380 Planarity : 0.005 0.039 2660 Dihedral : 4.023 16.200 2100 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 5.62 % Allowed : 25.07 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.20), residues: 1876 helix: 1.75 (0.12), residues: 1764 sheet: None (None), residues: 0 loop : -6.00 (0.18), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 344 TYR 0.020 0.001 TYR G 284 PHE 0.017 0.001 PHE c 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14840) covalent geometry : angle 0.72018 / 0.33 (20076) hydrogen bonds : bond 0.02777 / 1.89 ( 1148) hydrogen bonds : angle 3.58928 / 2.51 ( 3444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 711 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 LEU cc_start: 0.8748 (mp) cc_final: 0.8376 (mp) REVERT: B 298 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8222 (mm-30) REVERT: B 305 LEU cc_start: 0.8966 (mm) cc_final: 0.8699 (mm) REVERT: B 324 LYS cc_start: 0.8907 (tmtt) cc_final: 0.8469 (tmtt) REVERT: B 332 GLN cc_start: 0.8316 (mm110) cc_final: 0.7873 (mm110) REVERT: B 334 ARG cc_start: 0.8564 (ttm170) cc_final: 0.7952 (mmm-85) REVERT: B 347 MET cc_start: 0.8484 (tpp) cc_final: 0.8281 (mmm) REVERT: C 290 LEU cc_start: 0.8319 (tt) cc_final: 0.7767 (tt) REVERT: C 294 GLU cc_start: 0.8061 (mp0) cc_final: 0.7495 (mp0) REVERT: C 307 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8112 (mm-40) REVERT: C 318 LEU cc_start: 0.8994 (tp) cc_final: 0.8605 (tp) REVERT: C 322 ASP cc_start: 0.8204 (m-30) cc_final: 0.7892 (m-30) REVERT: C 329 ASN cc_start: 0.8346 (p0) cc_final: 0.8104 (p0) REVERT: C 332 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7867 (mm-40) REVERT: C 336 LEU cc_start: 0.9207 (tp) cc_final: 0.8995 (tp) REVERT: C 344 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7832 (ttm110) REVERT: C 347 MET cc_start: 0.8382 (tpp) cc_final: 0.8162 (tpp) REVERT: D 291 LEU cc_start: 0.8749 (tp) cc_final: 0.8436 (tp) REVERT: D 307 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8204 (mm-40) REVERT: D 322 ASP cc_start: 0.8038 (m-30) cc_final: 0.7684 (m-30) REVERT: D 323 ILE cc_start: 0.8746 (mt) cc_final: 0.8535 (mt) REVERT: D 337 SER cc_start: 0.8982 (m) cc_final: 0.8702 (p) REVERT: D 347 MET cc_start: 0.8416 (tpp) cc_final: 0.7409 (tpp) REVERT: D 350 ARG cc_start: 0.8217 (ttm170) cc_final: 0.7943 (ttm170) REVERT: E 294 GLU cc_start: 0.8129 (mp0) cc_final: 0.7716 (mp0) REVERT: E 298 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7802 (mm-30) REVERT: E 329 ASN cc_start: 0.8306 (p0) cc_final: 0.8066 (p0) REVERT: E 347 MET cc_start: 0.8363 (tpp) cc_final: 0.8030 (mpp) REVERT: F 315 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8384 (tt) REVERT: F 337 SER cc_start: 0.8979 (m) cc_final: 0.8488 (t) REVERT: F 341 SER cc_start: 0.8863 (m) cc_final: 0.8330 (p) REVERT: F 347 MET cc_start: 0.8001 (mpp) cc_final: 0.7692 (mpp) REVERT: F 350 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8321 (ttm170) REVERT: G 286 GLU cc_start: 0.8312 (pm20) cc_final: 0.8085 (pm20) REVERT: G 288 LEU cc_start: 0.8920 (mp) cc_final: 0.8631 (mp) REVERT: G 292 ARG cc_start: 0.8321 (mtt90) cc_final: 0.7943 (mtt90) REVERT: G 318 LEU cc_start: 0.8757 (tp) cc_final: 0.8502 (tp) REVERT: G 322 ASP cc_start: 0.8444 (m-30) cc_final: 0.7938 (m-30) REVERT: G 323 ILE cc_start: 0.8821 (mt) cc_final: 0.8612 (mt) REVERT: G 334 ARG cc_start: 0.8763 (ttm170) cc_final: 0.7989 (mtm-85) REVERT: G 337 SER cc_start: 0.8979 (m) cc_final: 0.8537 (t) REVERT: G 341 SER cc_start: 0.8906 (m) cc_final: 0.8503 (p) REVERT: G 344 ARG cc_start: 0.8244 (ttp-110) cc_final: 0.7514 (mtp-110) REVERT: G 347 MET cc_start: 0.8251 (tpp) cc_final: 0.7720 (mpp) REVERT: H 301 LEU cc_start: 0.8709 (tp) cc_final: 0.8423 (tp) REVERT: H 305 LEU cc_start: 0.8938 (mm) cc_final: 0.8677 (mm) REVERT: H 312 PRO cc_start: 0.8786 (Cg_exo) cc_final: 0.8531 (Cg_endo) REVERT: H 314 VAL cc_start: 0.8548 (t) cc_final: 0.8212 (m) REVERT: H 322 ASP cc_start: 0.8483 (m-30) cc_final: 0.7819 (m-30) REVERT: H 334 ARG cc_start: 0.8319 (mmm-85) cc_final: 0.7374 (mmm-85) REVERT: H 337 SER cc_start: 0.8867 (m) cc_final: 0.8651 (p) REVERT: H 344 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7407 (ttm170) REVERT: H 347 MET cc_start: 0.8494 (tpp) cc_final: 0.7458 (mpp) REVERT: H 350 ARG cc_start: 0.8338 (ttm170) cc_final: 0.7956 (ttm170) REVERT: I 294 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: I 318 LEU cc_start: 0.8915 (tp) cc_final: 0.8674 (tp) REVERT: I 322 ASP cc_start: 0.8259 (m-30) cc_final: 0.6996 (m-30) REVERT: I 334 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.8269 (mmm-85) REVERT: I 348 GLN cc_start: 0.8305 (mt0) cc_final: 0.8063 (mt0) REVERT: J 286 GLU cc_start: 0.8281 (pm20) cc_final: 0.8042 (pm20) REVERT: J 334 ARG cc_start: 0.8404 (ttm170) cc_final: 0.7869 (ttm170) REVERT: J 337 SER cc_start: 0.8864 (m) cc_final: 0.8519 (p) REVERT: K 292 ARG cc_start: 0.8633 (mtt90) cc_final: 0.8129 (mtt-85) REVERT: K 315 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8496 (tt) REVERT: K 322 ASP cc_start: 0.8402 (m-30) cc_final: 0.8075 (m-30) REVERT: K 347 MET cc_start: 0.8244 (mmm) cc_final: 0.7827 (tpp) REVERT: L 318 LEU cc_start: 0.8984 (tp) cc_final: 0.8750 (tp) REVERT: L 334 ARG cc_start: 0.8747 (ttm170) cc_final: 0.8421 (ttm170) REVERT: L 347 MET cc_start: 0.8330 (tpp) cc_final: 0.7343 (mpp) REVERT: L 350 ARG cc_start: 0.8522 (ttm170) cc_final: 0.8221 (ttm170) REVERT: M 292 ARG cc_start: 0.8509 (mtt90) cc_final: 0.8065 (mtt-85) REVERT: M 294 GLU cc_start: 0.8082 (mp0) cc_final: 0.7704 (mp0) REVERT: M 305 LEU cc_start: 0.8854 (mm) cc_final: 0.8514 (mm) REVERT: M 334 ARG cc_start: 0.8822 (ttm170) cc_final: 0.8500 (ttm170) REVERT: M 337 SER cc_start: 0.8939 (m) cc_final: 0.8601 (p) REVERT: N 305 LEU cc_start: 0.8951 (mm) cc_final: 0.8707 (mm) REVERT: N 307 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8024 (mm-40) REVERT: N 347 MET cc_start: 0.8294 (tpp) cc_final: 0.7946 (mpp) REVERT: O 292 ARG cc_start: 0.8728 (mtm-85) cc_final: 0.8386 (mtt-85) REVERT: O 343 CYS cc_start: 0.8644 (m) cc_final: 0.8334 (m) REVERT: O 347 MET cc_start: 0.8631 (tpp) cc_final: 0.8411 (tpp) REVERT: P 287 PHE cc_start: 0.8445 (t80) cc_final: 0.8173 (t80) REVERT: P 290 LEU cc_start: 0.8344 (tt) cc_final: 0.7974 (tt) REVERT: P 294 GLU cc_start: 0.8176 (mp0) cc_final: 0.7509 (mp0) REVERT: P 337 SER cc_start: 0.8695 (m) cc_final: 0.8320 (p) REVERT: Q 334 ARG cc_start: 0.8701 (ttm170) cc_final: 0.7716 (mtm180) REVERT: Q 339 LEU cc_start: 0.8745 (mm) cc_final: 0.8366 (mm) REVERT: Q 343 CYS cc_start: 0.8610 (m) cc_final: 0.8232 (m) REVERT: R 294 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: R 305 LEU cc_start: 0.8961 (mm) cc_final: 0.8696 (mm) REVERT: R 307 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8284 (mm-40) REVERT: R 337 SER cc_start: 0.8864 (m) cc_final: 0.8522 (p) REVERT: R 348 GLN cc_start: 0.8239 (mt0) cc_final: 0.7941 (tt0) REVERT: S 318 LEU cc_start: 0.8765 (tp) cc_final: 0.8527 (tp) REVERT: S 324 LYS cc_start: 0.8875 (tmtt) cc_final: 0.8465 (tmtt) REVERT: S 332 GLN cc_start: 0.8521 (mm110) cc_final: 0.8172 (mm110) REVERT: S 334 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.7963 (mtt90) REVERT: S 337 SER cc_start: 0.8839 (m) cc_final: 0.8431 (p) REVERT: S 341 SER cc_start: 0.8754 (m) cc_final: 0.8387 (p) REVERT: S 350 ARG cc_start: 0.8658 (ttm170) cc_final: 0.8453 (ttm170) REVERT: T 324 LYS cc_start: 0.8890 (tmtt) cc_final: 0.8543 (tmtt) REVERT: T 334 ARG cc_start: 0.8227 (ttm170) cc_final: 0.7952 (mmm-85) REVERT: T 347 MET cc_start: 0.8447 (tpp) cc_final: 0.7967 (tpp) REVERT: U 294 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: U 301 LEU cc_start: 0.8750 (tp) cc_final: 0.8201 (tp) REVERT: U 305 LEU cc_start: 0.8830 (mm) cc_final: 0.8522 (mm) REVERT: U 334 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.8267 (ttm-80) REVERT: V 322 ASP cc_start: 0.8124 (m-30) cc_final: 0.7761 (m-30) REVERT: V 334 ARG cc_start: 0.8378 (ttm170) cc_final: 0.7858 (ttm170) REVERT: V 337 SER cc_start: 0.9038 (m) cc_final: 0.8722 (p) REVERT: V 344 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7564 (ttp-110) REVERT: W 286 GLU cc_start: 0.8148 (pm20) cc_final: 0.7863 (pm20) REVERT: W 291 LEU cc_start: 0.8783 (mp) cc_final: 0.8474 (mp) REVERT: W 305 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8752 (mm) REVERT: W 315 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8384 (tt) REVERT: W 347 MET cc_start: 0.8334 (tpp) cc_final: 0.7977 (mmm) REVERT: W 348 GLN cc_start: 0.8765 (tt0) cc_final: 0.8452 (tt0) REVERT: W 350 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7878 (ttm110) REVERT: X 305 LEU cc_start: 0.8999 (mm) cc_final: 0.8687 (mm) REVERT: X 307 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7972 (mm-40) REVERT: X 322 ASP cc_start: 0.8127 (m-30) cc_final: 0.7719 (m-30) REVERT: X 337 SER cc_start: 0.8843 (m) cc_final: 0.8623 (p) REVERT: X 347 MET cc_start: 0.8356 (tpp) cc_final: 0.7624 (mpp) REVERT: X 350 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7860 (ttm170) REVERT: Y 286 GLU cc_start: 0.8372 (pm20) cc_final: 0.8094 (pm20) REVERT: Y 292 ARG cc_start: 0.8552 (mtt90) cc_final: 0.8265 (mtt90) REVERT: Y 301 LEU cc_start: 0.8790 (tp) cc_final: 0.8347 (tp) REVERT: Y 304 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8480 (mm) REVERT: Y 305 LEU cc_start: 0.9061 (mm) cc_final: 0.8750 (mm) REVERT: Y 323 ILE cc_start: 0.8468 (mp) cc_final: 0.8204 (mp) REVERT: Y 329 ASN cc_start: 0.8429 (p0) cc_final: 0.8146 (p0) REVERT: Z 294 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: Z 304 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7890 (mm) REVERT: Z 334 ARG cc_start: 0.8650 (ttm170) cc_final: 0.8028 (ttm-80) REVERT: Z 337 SER cc_start: 0.8748 (m) cc_final: 0.8467 (p) REVERT: Z 338 ARG cc_start: 0.8615 (tpp80) cc_final: 0.8110 (mmm-85) REVERT: Z 348 GLN cc_start: 0.8437 (mt0) cc_final: 0.8055 (mt0) REVERT: a 347 MET cc_start: 0.8179 (tpp) cc_final: 0.7390 (tpp) REVERT: b 318 LEU cc_start: 0.8975 (tp) cc_final: 0.8451 (mt) REVERT: b 347 MET cc_start: 0.8156 (tpp) cc_final: 0.7482 (tpp) REVERT: c 291 LEU cc_start: 0.9192 (mp) cc_final: 0.8971 (mp) REVERT: c 304 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8073 (mm) REVERT: c 334 ARG cc_start: 0.8666 (ttm170) cc_final: 0.8133 (mtt90) outliers start: 85 outliers final: 56 residues processed: 724 average time/residue: 0.1619 time to fit residues: 158.5949 Evaluate side-chains 781 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 711 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 350 ARG Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 315 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 304 LEU Chi-restraints excluded: chain L residue 315 LEU Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 315 LEU Chi-restraints excluded: chain N residue 323 ILE Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain O residue 304 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain Q residue 290 LEU Chi-restraints excluded: chain Q residue 291 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 315 LEU Chi-restraints excluded: chain Q residue 350 ARG Chi-restraints excluded: chain R residue 286 GLU Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain S residue 290 LEU Chi-restraints excluded: chain S residue 317 THR Chi-restraints excluded: chain S residue 339 LEU Chi-restraints excluded: chain T residue 291 LEU Chi-restraints excluded: chain T residue 304 LEU Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 294 GLU Chi-restraints excluded: chain V residue 304 LEU Chi-restraints excluded: chain V residue 348 GLN Chi-restraints excluded: chain W residue 304 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 315 LEU Chi-restraints excluded: chain W residue 350 ARG Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain Y residue 291 LEU Chi-restraints excluded: chain Y residue 304 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 317 THR Chi-restraints excluded: chain Z residue 294 GLU Chi-restraints excluded: chain Z residue 304 LEU Chi-restraints excluded: chain a residue 304 LEU Chi-restraints excluded: chain c residue 304 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 52 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 0.0570 chunk 101 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 332 GLN E 348 GLN F 352 GLN G 352 GLN ** H 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 332 GLN I 352 GLN M 332 GLN Q 332 GLN ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 348 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.123393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.107962 restraints weight = 25798.070| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.27 r_work: 0.3480 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14840 Z= 0.144 Angle : 0.730 10.560 20076 Z= 0.332 Chirality : 0.040 0.262 2380 Planarity : 0.005 0.041 2660 Dihedral : 4.042 16.154 2100 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 5.16 % Allowed : 26.06 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.20), residues: 1876 helix: 1.71 (0.12), residues: 1764 sheet: None (None), residues: 0 loop : -5.89 (0.19), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 344 TYR 0.021 0.001 TYR G 284 PHE 0.018 0.001 PHE N 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14840) covalent geometry : angle 0.72963 / 0.33 (20076) hydrogen bonds : bond 0.02806 / 1.91 ( 1148) hydrogen bonds : angle 3.61896 / 2.53 ( 3444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 715 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 LEU cc_start: 0.8767 (mp) cc_final: 0.8408 (mp) REVERT: B 298 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8258 (mm-30) REVERT: B 305 LEU cc_start: 0.8978 (mm) cc_final: 0.8713 (mm) REVERT: B 324 LYS cc_start: 0.8897 (tmtt) cc_final: 0.8469 (tmtt) REVERT: B 329 ASN cc_start: 0.8264 (p0) cc_final: 0.8037 (p0) REVERT: B 332 GLN cc_start: 0.8164 (mm110) cc_final: 0.7827 (mm-40) REVERT: B 334 ARG cc_start: 0.8576 (ttm170) cc_final: 0.8135 (mmm-85) REVERT: B 347 MET cc_start: 0.8523 (tpp) cc_final: 0.8315 (mmm) REVERT: C 290 LEU cc_start: 0.8318 (tt) cc_final: 0.7754 (tt) REVERT: C 294 GLU cc_start: 0.7973 (mp0) cc_final: 0.7421 (mp0) REVERT: C 307 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8109 (mm-40) REVERT: C 318 LEU cc_start: 0.8974 (tp) cc_final: 0.8598 (tp) REVERT: C 322 ASP cc_start: 0.8240 (m-30) cc_final: 0.7920 (m-30) REVERT: C 329 ASN cc_start: 0.8389 (p0) cc_final: 0.8165 (p0) REVERT: C 332 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7847 (mm-40) REVERT: C 336 LEU cc_start: 0.9217 (tp) cc_final: 0.9011 (tp) REVERT: C 347 MET cc_start: 0.8393 (tpp) cc_final: 0.8174 (tpp) REVERT: D 307 GLN cc_start: 0.8543 (mm-40) cc_final: 0.7997 (mm-40) REVERT: D 322 ASP cc_start: 0.8051 (m-30) cc_final: 0.7750 (m-30) REVERT: D 323 ILE cc_start: 0.8753 (mt) cc_final: 0.8528 (mt) REVERT: D 337 SER cc_start: 0.8982 (m) cc_final: 0.8704 (p) REVERT: D 347 MET cc_start: 0.8404 (tpp) cc_final: 0.7460 (tpp) REVERT: D 350 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7931 (ttm170) REVERT: E 294 GLU cc_start: 0.8133 (mp0) cc_final: 0.7735 (mp0) REVERT: E 298 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7806 (mm-30) REVERT: E 329 ASN cc_start: 0.8313 (p0) cc_final: 0.8058 (p0) REVERT: E 347 MET cc_start: 0.8342 (tpp) cc_final: 0.7931 (mpp) REVERT: F 315 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8359 (tt) REVERT: F 337 SER cc_start: 0.8980 (m) cc_final: 0.8485 (t) REVERT: F 341 SER cc_start: 0.8844 (m) cc_final: 0.8299 (p) REVERT: F 347 MET cc_start: 0.8018 (mpp) cc_final: 0.7786 (mpp) REVERT: G 286 GLU cc_start: 0.8361 (pm20) cc_final: 0.8125 (pm20) REVERT: G 288 LEU cc_start: 0.8938 (mp) cc_final: 0.8643 (mp) REVERT: G 292 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7960 (mtt90) REVERT: G 318 LEU cc_start: 0.8764 (tp) cc_final: 0.8449 (tp) REVERT: G 322 ASP cc_start: 0.8467 (m-30) cc_final: 0.7871 (m-30) REVERT: G 323 ILE cc_start: 0.8826 (mt) cc_final: 0.8607 (mt) REVERT: G 332 GLN cc_start: 0.8464 (mm110) cc_final: 0.8203 (mm110) REVERT: G 334 ARG cc_start: 0.8794 (ttm170) cc_final: 0.7739 (mtt180) REVERT: G 337 SER cc_start: 0.9003 (m) cc_final: 0.8579 (t) REVERT: G 341 SER cc_start: 0.8921 (m) cc_final: 0.8516 (p) REVERT: G 344 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7518 (mtp-110) REVERT: G 347 MET cc_start: 0.8259 (tpp) cc_final: 0.7721 (mpp) REVERT: H 301 LEU cc_start: 0.8700 (tp) cc_final: 0.8408 (tp) REVERT: H 305 LEU cc_start: 0.8930 (mm) cc_final: 0.8670 (mm) REVERT: H 306 GLN cc_start: 0.8671 (tt0) cc_final: 0.8465 (tt0) REVERT: H 312 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.8547 (Cg_endo) REVERT: H 322 ASP cc_start: 0.8469 (m-30) cc_final: 0.7697 (m-30) REVERT: H 334 ARG cc_start: 0.8326 (mmm-85) cc_final: 0.7373 (mmm-85) REVERT: H 337 SER cc_start: 0.8876 (m) cc_final: 0.8660 (p) REVERT: H 344 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7377 (ttm170) REVERT: H 347 MET cc_start: 0.8489 (tpp) cc_final: 0.7422 (mpp) REVERT: H 350 ARG cc_start: 0.8394 (ttm170) cc_final: 0.8008 (ttm170) REVERT: I 318 LEU cc_start: 0.8907 (tp) cc_final: 0.8664 (tp) REVERT: I 322 ASP cc_start: 0.8261 (m-30) cc_final: 0.7026 (m-30) REVERT: I 334 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8247 (mmm-85) REVERT: I 348 GLN cc_start: 0.8285 (mt0) cc_final: 0.8039 (mt0) REVERT: J 286 GLU cc_start: 0.8298 (pm20) cc_final: 0.8070 (pm20) REVERT: J 334 ARG cc_start: 0.8426 (ttm170) cc_final: 0.7884 (ttm170) REVERT: J 337 SER cc_start: 0.8872 (m) cc_final: 0.8519 (p) REVERT: K 292 ARG cc_start: 0.8659 (mtt90) cc_final: 0.8132 (mtt-85) REVERT: K 307 GLN cc_start: 0.8742 (mm110) cc_final: 0.8536 (mm110) REVERT: K 315 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8497 (tt) REVERT: K 322 ASP cc_start: 0.8393 (m-30) cc_final: 0.8053 (m-30) REVERT: K 337 SER cc_start: 0.8953 (m) cc_final: 0.8715 (p) REVERT: K 347 MET cc_start: 0.8260 (mmm) cc_final: 0.7834 (tpp) REVERT: L 318 LEU cc_start: 0.8968 (tp) cc_final: 0.8731 (tp) REVERT: L 334 ARG cc_start: 0.8731 (ttm170) cc_final: 0.8391 (ttm170) REVERT: L 347 MET cc_start: 0.8325 (tpp) cc_final: 0.7317 (mpp) REVERT: L 350 ARG cc_start: 0.8553 (ttm170) cc_final: 0.8237 (ttm170) REVERT: M 292 ARG cc_start: 0.8533 (mtt90) cc_final: 0.8099 (mtt-85) REVERT: M 294 GLU cc_start: 0.8071 (mp0) cc_final: 0.7689 (mp0) REVERT: M 305 LEU cc_start: 0.8883 (mm) cc_final: 0.8544 (mm) REVERT: M 334 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8503 (ttm170) REVERT: M 337 SER cc_start: 0.8934 (m) cc_final: 0.8593 (p) REVERT: N 305 LEU cc_start: 0.8946 (mm) cc_final: 0.8703 (mm) REVERT: N 307 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8026 (mm-40) REVERT: N 347 MET cc_start: 0.8332 (tpp) cc_final: 0.7884 (mpp) REVERT: O 292 ARG cc_start: 0.8741 (mtm-85) cc_final: 0.8384 (mtt-85) REVERT: O 343 CYS cc_start: 0.8658 (m) cc_final: 0.8318 (m) REVERT: O 347 MET cc_start: 0.8651 (tpp) cc_final: 0.8391 (tpp) REVERT: P 287 PHE cc_start: 0.8446 (t80) cc_final: 0.8169 (t80) REVERT: P 290 LEU cc_start: 0.8333 (tt) cc_final: 0.7954 (tt) REVERT: P 294 GLU cc_start: 0.8172 (mp0) cc_final: 0.7497 (mp0) REVERT: P 337 SER cc_start: 0.8713 (m) cc_final: 0.8341 (p) REVERT: Q 334 ARG cc_start: 0.8706 (ttm170) cc_final: 0.7724 (mtm180) REVERT: Q 339 LEU cc_start: 0.8736 (mm) cc_final: 0.8357 (mm) REVERT: Q 343 CYS cc_start: 0.8639 (m) cc_final: 0.8255 (m) REVERT: R 294 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: R 305 LEU cc_start: 0.8968 (mm) cc_final: 0.8703 (mm) REVERT: R 307 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8288 (mm-40) REVERT: R 337 SER cc_start: 0.8852 (m) cc_final: 0.8509 (p) REVERT: R 348 GLN cc_start: 0.8281 (mt0) cc_final: 0.7990 (tt0) REVERT: S 294 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: S 318 LEU cc_start: 0.8743 (tp) cc_final: 0.8504 (tp) REVERT: S 324 LYS cc_start: 0.8886 (tmtt) cc_final: 0.8477 (tmtt) REVERT: S 332 GLN cc_start: 0.8533 (mm110) cc_final: 0.8189 (mm110) REVERT: S 334 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.7973 (mtt90) REVERT: S 337 SER cc_start: 0.8844 (m) cc_final: 0.8436 (p) REVERT: S 341 SER cc_start: 0.8747 (m) cc_final: 0.8377 (p) REVERT: S 350 ARG cc_start: 0.8665 (ttm170) cc_final: 0.8408 (ttm170) REVERT: T 324 LYS cc_start: 0.8896 (tmtt) cc_final: 0.8573 (tmtt) REVERT: T 334 ARG cc_start: 0.8317 (ttm170) cc_final: 0.7850 (mmm-85) REVERT: T 347 MET cc_start: 0.8452 (tpp) cc_final: 0.7959 (tpp) REVERT: U 294 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: U 301 LEU cc_start: 0.8798 (tp) cc_final: 0.8246 (tp) REVERT: U 304 LEU cc_start: 0.8625 (mm) cc_final: 0.8346 (mm) REVERT: U 305 LEU cc_start: 0.8850 (mm) cc_final: 0.8515 (mm) REVERT: U 334 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.8266 (ttm-80) REVERT: U 347 MET cc_start: 0.8240 (tpp) cc_final: 0.7915 (mpp) REVERT: V 322 ASP cc_start: 0.8151 (m-30) cc_final: 0.7772 (m-30) REVERT: V 334 ARG cc_start: 0.8342 (ttm170) cc_final: 0.7839 (ttm170) REVERT: V 337 SER cc_start: 0.9016 (m) cc_final: 0.8780 (p) REVERT: V 344 ARG cc_start: 0.7903 (ttp-110) cc_final: 0.7555 (ttp-110) REVERT: W 291 LEU cc_start: 0.8779 (mp) cc_final: 0.8467 (mp) REVERT: W 305 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8754 (mm) REVERT: W 315 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8398 (tt) REVERT: W 347 MET cc_start: 0.8358 (tpp) cc_final: 0.7989 (mmm) REVERT: W 348 GLN cc_start: 0.8763 (tt0) cc_final: 0.8440 (tt0) REVERT: W 350 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7914 (ttm110) REVERT: X 305 LEU cc_start: 0.8995 (mm) cc_final: 0.8677 (mm) REVERT: X 307 GLN cc_start: 0.8542 (mm-40) cc_final: 0.7997 (mm-40) REVERT: X 322 ASP cc_start: 0.8137 (m-30) cc_final: 0.7727 (m-30) REVERT: X 337 SER cc_start: 0.8843 (m) cc_final: 0.8622 (p) REVERT: X 347 MET cc_start: 0.8378 (tpp) cc_final: 0.7643 (mpp) REVERT: X 350 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7920 (ttm170) REVERT: Y 286 GLU cc_start: 0.8388 (pm20) cc_final: 0.8114 (pm20) REVERT: Y 292 ARG cc_start: 0.8576 (mtt90) cc_final: 0.8294 (mtt90) REVERT: Y 301 LEU cc_start: 0.8820 (tp) cc_final: 0.8391 (tp) REVERT: Y 304 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8494 (mm) REVERT: Y 305 LEU cc_start: 0.9066 (mm) cc_final: 0.8760 (mm) REVERT: Y 323 ILE cc_start: 0.8479 (mt) cc_final: 0.8219 (mp) REVERT: Y 329 ASN cc_start: 0.8432 (p0) cc_final: 0.8151 (p0) REVERT: Z 291 LEU cc_start: 0.9000 (mp) cc_final: 0.8660 (mp) REVERT: Z 294 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: Z 304 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7869 (mm) REVERT: Z 334 ARG cc_start: 0.8653 (ttm170) cc_final: 0.8027 (ttm-80) REVERT: Z 337 SER cc_start: 0.8738 (m) cc_final: 0.8460 (p) REVERT: Z 338 ARG cc_start: 0.8619 (tpp80) cc_final: 0.8111 (mmm-85) REVERT: Z 348 GLN cc_start: 0.8446 (mt0) cc_final: 0.8064 (mt0) REVERT: a 347 MET cc_start: 0.8223 (tpp) cc_final: 0.7476 (tpp) REVERT: b 318 LEU cc_start: 0.8954 (tp) cc_final: 0.8454 (mt) REVERT: b 347 MET cc_start: 0.8171 (tpp) cc_final: 0.7516 (tpp) REVERT: c 291 LEU cc_start: 0.9197 (mp) cc_final: 0.8974 (mp) REVERT: c 304 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8089 (mm) REVERT: c 334 ARG cc_start: 0.8664 (ttm170) cc_final: 0.8133 (mtt90) REVERT: c 347 MET cc_start: 0.8243 (tpp) cc_final: 0.7729 (tpp) outliers start: 78 outliers final: 57 residues processed: 728 average time/residue: 0.1636 time to fit residues: 161.1235 Evaluate side-chains 782 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 712 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 315 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 304 LEU Chi-restraints excluded: chain L residue 315 LEU Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 350 ARG Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 315 LEU Chi-restraints excluded: chain N residue 323 ILE Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain O residue 304 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 315 LEU Chi-restraints excluded: chain Q residue 350 ARG Chi-restraints excluded: chain R residue 286 GLU Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain S residue 290 LEU Chi-restraints excluded: chain S residue 294 GLU Chi-restraints excluded: chain S residue 317 THR Chi-restraints excluded: chain S residue 339 LEU Chi-restraints excluded: chain T residue 291 LEU Chi-restraints excluded: chain T residue 304 LEU Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 294 GLU Chi-restraints excluded: chain V residue 304 LEU Chi-restraints excluded: chain V residue 348 GLN Chi-restraints excluded: chain W residue 304 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 315 LEU Chi-restraints excluded: chain W residue 350 ARG Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain X residue 314 VAL Chi-restraints excluded: chain Y residue 291 LEU Chi-restraints excluded: chain Y residue 304 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 317 THR Chi-restraints excluded: chain Z residue 294 GLU Chi-restraints excluded: chain Z residue 304 LEU Chi-restraints excluded: chain a residue 304 LEU Chi-restraints excluded: chain b residue 291 LEU Chi-restraints excluded: chain c residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 12 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 332 GLN ** H 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN O 352 GLN ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.125692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.110383 restraints weight = 25590.143| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.36 r_work: 0.3468 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14840 Z= 0.159 Angle : 0.754 16.131 20076 Z= 0.343 Chirality : 0.041 0.254 2380 Planarity : 0.005 0.044 2660 Dihedral : 4.118 17.035 2100 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 4.83 % Allowed : 26.85 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.20), residues: 1876 helix: 1.63 (0.12), residues: 1764 sheet: None (None), residues: 0 loop : -5.74 (0.21), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 344 TYR 0.021 0.001 TYR G 284 PHE 0.021 0.001 PHE N 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (14840) covalent geometry : angle 0.75359 / 0.34 (20076) hydrogen bonds : bond 0.02955 / 2.02 ( 1148) hydrogen bonds : angle 3.68346 / 2.57 ( 3444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 714 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 LEU cc_start: 0.8778 (mp) cc_final: 0.8417 (mp) REVERT: B 294 GLU cc_start: 0.7938 (mp0) cc_final: 0.7683 (mp0) REVERT: B 298 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8273 (mm-30) REVERT: B 305 LEU cc_start: 0.8977 (mm) cc_final: 0.8708 (mm) REVERT: B 324 LYS cc_start: 0.8904 (tmtt) cc_final: 0.8475 (tmtt) REVERT: B 332 GLN cc_start: 0.8209 (mm110) cc_final: 0.7874 (mm110) REVERT: B 334 ARG cc_start: 0.8617 (ttm170) cc_final: 0.8163 (mmm-85) REVERT: B 347 MET cc_start: 0.8544 (tpp) cc_final: 0.8325 (mmm) REVERT: C 290 LEU cc_start: 0.8323 (tt) cc_final: 0.7751 (tt) REVERT: C 292 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7956 (mtt90) REVERT: C 294 GLU cc_start: 0.7964 (mp0) cc_final: 0.7375 (mp0) REVERT: C 305 LEU cc_start: 0.8945 (mm) cc_final: 0.8741 (mm) REVERT: C 307 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8096 (mm-40) REVERT: C 318 LEU cc_start: 0.8995 (tp) cc_final: 0.8617 (tp) REVERT: C 322 ASP cc_start: 0.8241 (m-30) cc_final: 0.7940 (m-30) REVERT: C 329 ASN cc_start: 0.8358 (p0) cc_final: 0.8146 (p0) REVERT: C 336 LEU cc_start: 0.9211 (tp) cc_final: 0.9010 (tp) REVERT: C 347 MET cc_start: 0.8415 (tpp) cc_final: 0.8201 (tpp) REVERT: D 291 LEU cc_start: 0.8752 (tp) cc_final: 0.8435 (tp) REVERT: D 307 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8202 (mm-40) REVERT: D 322 ASP cc_start: 0.8073 (m-30) cc_final: 0.7738 (m-30) REVERT: D 323 ILE cc_start: 0.8760 (mt) cc_final: 0.8533 (mt) REVERT: D 329 ASN cc_start: 0.8294 (p0) cc_final: 0.8028 (p0) REVERT: D 334 ARG cc_start: 0.8617 (tpp80) cc_final: 0.7806 (mmm-85) REVERT: D 337 SER cc_start: 0.8992 (m) cc_final: 0.8718 (p) REVERT: D 347 MET cc_start: 0.8372 (tpp) cc_final: 0.7437 (tpp) REVERT: D 350 ARG cc_start: 0.8219 (ttm170) cc_final: 0.7968 (ttm170) REVERT: E 294 GLU cc_start: 0.8133 (mp0) cc_final: 0.7697 (mp0) REVERT: E 298 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7808 (mm-30) REVERT: E 329 ASN cc_start: 0.8320 (p0) cc_final: 0.8058 (p0) REVERT: E 347 MET cc_start: 0.8334 (tpp) cc_final: 0.7930 (mpp) REVERT: F 315 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8345 (tt) REVERT: F 337 SER cc_start: 0.8988 (m) cc_final: 0.8520 (t) REVERT: F 341 SER cc_start: 0.8851 (m) cc_final: 0.8297 (p) REVERT: G 286 GLU cc_start: 0.8350 (pm20) cc_final: 0.8112 (pm20) REVERT: G 288 LEU cc_start: 0.8937 (mp) cc_final: 0.8624 (mp) REVERT: G 292 ARG cc_start: 0.8377 (mtt90) cc_final: 0.7979 (mtt90) REVERT: G 318 LEU cc_start: 0.8710 (tp) cc_final: 0.8486 (tp) REVERT: G 322 ASP cc_start: 0.8462 (m-30) cc_final: 0.7957 (m-30) REVERT: G 323 ILE cc_start: 0.8854 (mt) cc_final: 0.8621 (mt) REVERT: G 332 GLN cc_start: 0.8480 (mm110) cc_final: 0.8246 (mm110) REVERT: G 334 ARG cc_start: 0.8785 (ttm170) cc_final: 0.7740 (mtt180) REVERT: G 337 SER cc_start: 0.9014 (m) cc_final: 0.8584 (t) REVERT: G 341 SER cc_start: 0.8915 (m) cc_final: 0.8499 (p) REVERT: G 344 ARG cc_start: 0.8298 (ttp-110) cc_final: 0.7539 (mtp-110) REVERT: G 347 MET cc_start: 0.8268 (tpp) cc_final: 0.7728 (mpp) REVERT: H 301 LEU cc_start: 0.8707 (tp) cc_final: 0.8421 (tp) REVERT: H 305 LEU cc_start: 0.8934 (mm) cc_final: 0.8674 (mm) REVERT: H 306 GLN cc_start: 0.8676 (tt0) cc_final: 0.8472 (tt0) REVERT: H 312 PRO cc_start: 0.8821 (Cg_exo) cc_final: 0.8560 (Cg_endo) REVERT: H 314 VAL cc_start: 0.8580 (t) cc_final: 0.8056 (p) REVERT: H 322 ASP cc_start: 0.8477 (m-30) cc_final: 0.7743 (m-30) REVERT: H 334 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.7406 (mmm-85) REVERT: H 337 SER cc_start: 0.8890 (m) cc_final: 0.8675 (p) REVERT: H 347 MET cc_start: 0.8503 (tpp) cc_final: 0.7448 (mpp) REVERT: H 350 ARG cc_start: 0.8411 (ttm170) cc_final: 0.8029 (ttm170) REVERT: I 294 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: I 318 LEU cc_start: 0.8903 (tp) cc_final: 0.8652 (tp) REVERT: I 322 ASP cc_start: 0.8261 (m-30) cc_final: 0.7047 (m-30) REVERT: I 324 LYS cc_start: 0.9053 (tmtt) cc_final: 0.8657 (tmtt) REVERT: I 334 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8218 (mmm-85) REVERT: I 347 MET cc_start: 0.8031 (tpp) cc_final: 0.7771 (tpp) REVERT: I 348 GLN cc_start: 0.8325 (mt0) cc_final: 0.8075 (mt0) REVERT: J 286 GLU cc_start: 0.8313 (pm20) cc_final: 0.8089 (pm20) REVERT: J 334 ARG cc_start: 0.8451 (ttm170) cc_final: 0.7871 (ttm170) REVERT: J 337 SER cc_start: 0.8897 (m) cc_final: 0.8533 (p) REVERT: K 292 ARG cc_start: 0.8677 (mtt90) cc_final: 0.8125 (mtt-85) REVERT: K 307 GLN cc_start: 0.8755 (mm110) cc_final: 0.8549 (mm110) REVERT: K 315 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8496 (tt) REVERT: K 322 ASP cc_start: 0.8420 (m-30) cc_final: 0.8068 (m-30) REVERT: K 347 MET cc_start: 0.8306 (mmm) cc_final: 0.7870 (tpp) REVERT: L 318 LEU cc_start: 0.8963 (tp) cc_final: 0.8718 (tp) REVERT: L 334 ARG cc_start: 0.8737 (ttm170) cc_final: 0.8376 (ttm170) REVERT: M 294 GLU cc_start: 0.8089 (mp0) cc_final: 0.7750 (mp0) REVERT: M 305 LEU cc_start: 0.8885 (mm) cc_final: 0.8551 (mm) REVERT: M 334 ARG cc_start: 0.8853 (ttm170) cc_final: 0.8550 (ttm170) REVERT: M 337 SER cc_start: 0.8968 (m) cc_final: 0.8764 (m) REVERT: N 305 LEU cc_start: 0.8943 (mm) cc_final: 0.8705 (mm) REVERT: N 307 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8057 (mm-40) REVERT: N 347 MET cc_start: 0.8372 (tpp) cc_final: 0.7887 (mpp) REVERT: O 292 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8364 (mtt-85) REVERT: O 343 CYS cc_start: 0.8669 (m) cc_final: 0.8363 (m) REVERT: P 287 PHE cc_start: 0.8460 (t80) cc_final: 0.8181 (t80) REVERT: P 334 ARG cc_start: 0.8744 (ttm170) cc_final: 0.8236 (ttm170) REVERT: P 337 SER cc_start: 0.8727 (m) cc_final: 0.8333 (p) REVERT: Q 334 ARG cc_start: 0.8725 (ttm170) cc_final: 0.7752 (mtm180) REVERT: Q 339 LEU cc_start: 0.8757 (mm) cc_final: 0.8411 (mm) REVERT: Q 343 CYS cc_start: 0.8654 (m) cc_final: 0.8289 (m) REVERT: R 294 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: R 305 LEU cc_start: 0.8972 (mm) cc_final: 0.8693 (mm) REVERT: R 307 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8292 (mm-40) REVERT: R 337 SER cc_start: 0.8882 (m) cc_final: 0.8612 (p) REVERT: R 348 GLN cc_start: 0.8281 (mt0) cc_final: 0.7986 (tt0) REVERT: S 294 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: S 318 LEU cc_start: 0.8756 (tp) cc_final: 0.8515 (tp) REVERT: S 324 LYS cc_start: 0.8880 (tmtt) cc_final: 0.8476 (tmtt) REVERT: S 332 GLN cc_start: 0.8551 (mm110) cc_final: 0.8332 (mm110) REVERT: S 334 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.7997 (mtt90) REVERT: S 337 SER cc_start: 0.8836 (m) cc_final: 0.8419 (p) REVERT: S 341 SER cc_start: 0.8774 (m) cc_final: 0.8397 (p) REVERT: S 350 ARG cc_start: 0.8677 (ttm170) cc_final: 0.8416 (ttm170) REVERT: T 324 LYS cc_start: 0.8895 (tmtt) cc_final: 0.8550 (tmtt) REVERT: T 334 ARG cc_start: 0.8242 (ttm170) cc_final: 0.7951 (mmm-85) REVERT: T 347 MET cc_start: 0.8468 (tpp) cc_final: 0.7976 (tpp) REVERT: U 294 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: U 301 LEU cc_start: 0.8812 (tp) cc_final: 0.8260 (tp) REVERT: U 304 LEU cc_start: 0.8601 (mm) cc_final: 0.8312 (mm) REVERT: U 305 LEU cc_start: 0.8886 (mm) cc_final: 0.8555 (mm) REVERT: U 334 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.8265 (ttm-80) REVERT: U 347 MET cc_start: 0.8181 (tpp) cc_final: 0.7803 (mpp) REVERT: V 294 GLU cc_start: 0.7917 (mp0) cc_final: 0.7462 (mp0) REVERT: V 322 ASP cc_start: 0.8114 (m-30) cc_final: 0.7747 (m-30) REVERT: V 334 ARG cc_start: 0.8311 (ttm170) cc_final: 0.7812 (ttm170) REVERT: V 337 SER cc_start: 0.9104 (m) cc_final: 0.8851 (p) REVERT: V 344 ARG cc_start: 0.7929 (ttp-110) cc_final: 0.7603 (ttp-110) REVERT: W 291 LEU cc_start: 0.8784 (mp) cc_final: 0.8468 (mp) REVERT: W 305 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8754 (mm) REVERT: W 315 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8415 (tt) REVERT: W 334 ARG cc_start: 0.8592 (ttm170) cc_final: 0.7948 (mmm-85) REVERT: W 347 MET cc_start: 0.8396 (tpp) cc_final: 0.7770 (mpp) REVERT: W 348 GLN cc_start: 0.8765 (tt0) cc_final: 0.8410 (tt0) REVERT: X 305 LEU cc_start: 0.8985 (mm) cc_final: 0.8673 (mm) REVERT: X 307 GLN cc_start: 0.8579 (mm-40) cc_final: 0.7963 (mm-40) REVERT: X 322 ASP cc_start: 0.8153 (m-30) cc_final: 0.7638 (m-30) REVERT: X 337 SER cc_start: 0.8831 (m) cc_final: 0.8594 (p) REVERT: X 347 MET cc_start: 0.8381 (tpp) cc_final: 0.7643 (mpp) REVERT: X 350 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7915 (ttm170) REVERT: Y 286 GLU cc_start: 0.8396 (pm20) cc_final: 0.8124 (pm20) REVERT: Y 292 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8345 (mtt90) REVERT: Y 301 LEU cc_start: 0.8792 (tp) cc_final: 0.8362 (tp) REVERT: Y 304 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8497 (mm) REVERT: Y 305 LEU cc_start: 0.9069 (mm) cc_final: 0.8760 (mm) REVERT: Y 323 ILE cc_start: 0.8489 (mt) cc_final: 0.8220 (mp) REVERT: Y 329 ASN cc_start: 0.8443 (p0) cc_final: 0.8159 (p0) REVERT: Z 291 LEU cc_start: 0.9002 (mp) cc_final: 0.8682 (mp) REVERT: Z 304 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7891 (mm) REVERT: Z 334 ARG cc_start: 0.8677 (ttm170) cc_final: 0.8056 (ttm-80) REVERT: Z 337 SER cc_start: 0.8754 (m) cc_final: 0.8484 (p) REVERT: Z 338 ARG cc_start: 0.8650 (tpp80) cc_final: 0.8141 (mmm-85) REVERT: a 347 MET cc_start: 0.8242 (tpp) cc_final: 0.7437 (tpp) REVERT: b 347 MET cc_start: 0.8169 (tpp) cc_final: 0.7527 (tpp) REVERT: c 291 LEU cc_start: 0.9214 (mp) cc_final: 0.8994 (mp) REVERT: c 304 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8106 (mm) REVERT: c 334 ARG cc_start: 0.8667 (ttm170) cc_final: 0.8143 (mtt90) REVERT: c 347 MET cc_start: 0.8247 (tpp) cc_final: 0.7726 (tpp) outliers start: 73 outliers final: 59 residues processed: 727 average time/residue: 0.1604 time to fit residues: 157.6612 Evaluate side-chains 784 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 714 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 315 LEU Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 304 LEU Chi-restraints excluded: chain L residue 315 LEU Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 350 ARG Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 315 LEU Chi-restraints excluded: chain N residue 323 ILE Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain O residue 304 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 305 LEU Chi-restraints excluded: chain Q residue 315 LEU Chi-restraints excluded: chain Q residue 350 ARG Chi-restraints excluded: chain R residue 286 GLU Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain S residue 290 LEU Chi-restraints excluded: chain S residue 294 GLU Chi-restraints excluded: chain S residue 317 THR Chi-restraints excluded: chain S residue 339 LEU Chi-restraints excluded: chain T residue 291 LEU Chi-restraints excluded: chain T residue 304 LEU Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 294 GLU Chi-restraints excluded: chain V residue 304 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain V residue 348 GLN Chi-restraints excluded: chain W residue 304 LEU Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 315 LEU Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 304 LEU Chi-restraints excluded: chain X residue 314 VAL Chi-restraints excluded: chain Y residue 291 LEU Chi-restraints excluded: chain Y residue 304 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 317 THR Chi-restraints excluded: chain Z residue 304 LEU Chi-restraints excluded: chain a residue 304 LEU Chi-restraints excluded: chain c residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 136 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 332 GLN ** H 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 GLN Q 332 GLN ** T 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.126088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.111993 restraints weight = 25761.378| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.27 r_work: 0.3479 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14840 Z= 0.165 Angle : 0.750 13.623 20076 Z= 0.342 Chirality : 0.041 0.267 2380 Planarity : 0.005 0.042 2660 Dihedral : 4.129 15.295 2100 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 4.89 % Allowed : 26.98 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.20), residues: 1876 helix: 1.60 (0.12), residues: 1764 sheet: None (None), residues: 0 loop : -5.66 (0.24), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 344 TYR 0.021 0.001 TYR G 284 PHE 0.021 0.001 PHE N 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (14840) covalent geometry : angle 0.75045 / 0.34 (20076) hydrogen bonds : bond 0.02999 / 2.05 ( 1148) hydrogen bonds : angle 3.69987 / 2.58 ( 3444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3735.63 seconds wall clock time: 64 minutes 47.40 seconds (3887.40 seconds total)