Starting phenix.real_space_refine on Sat Jul 4 03:52:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wbj_65841/07_2026/9wbj_65841.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wbj_65841/07_2026/9wbj_65841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wbj_65841/07_2026/9wbj_65841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wbj_65841/07_2026/9wbj_65841.map" model { file = "/net/cci-nas-00/data/ceres_data/9wbj_65841/07_2026/9wbj_65841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wbj_65841/07_2026/9wbj_65841.cif" } resolution = 3.37 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= 0.002 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 68 5.16 5 C 11152 2.51 5 N 3196 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 238 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: 17816 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: B, 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, d, e, f, g, h Time building chain proxies: 1.40, per 1000 atoms: 0.08 Number of scatterers: 17816 At special positions: 0 Unit cell: (83.83, 80.51, 311.25, 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 68 16.00 O 3400 8.00 N 3196 7.00 C 11152 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: 1.28 Conformation dependent library (CDL) restraints added in 737.5 milliseconds 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 0 sheets defined 84.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 319 through 327 Processing helix chain 'A' and resid 329 through 349 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 316 Processing helix chain 'B' and resid 319 through 327 Processing helix chain 'B' and resid 329 through 349 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 316 Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 329 through 349 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 316 Processing helix chain 'D' and resid 319 through 327 Processing helix chain 'D' and resid 329 through 349 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 316 Processing helix chain 'E' and resid 319 through 327 Processing helix chain 'E' and resid 329 through 349 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 316 Processing helix chain 'F' and resid 319 through 327 Processing helix chain 'F' and resid 329 through 349 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 316 Processing helix chain 'G' and resid 319 through 327 Processing helix chain 'G' and resid 329 through 349 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 316 Processing helix chain 'H' and resid 319 through 327 Processing helix chain 'H' and resid 329 through 349 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 316 Processing helix chain 'I' and resid 319 through 327 Processing helix chain 'I' and resid 329 through 349 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 316 Processing helix chain 'J' and resid 319 through 327 Processing helix chain 'J' and resid 329 through 349 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 316 Processing helix chain 'K' and resid 319 through 327 Processing helix chain 'K' and resid 329 through 349 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 316 Processing helix chain 'L' and resid 319 through 327 Processing helix chain 'L' and resid 329 through 349 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 316 Processing helix chain 'M' and resid 319 through 327 Processing helix chain 'M' and resid 329 through 349 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 316 Processing helix chain 'N' and resid 319 through 327 Processing helix chain 'N' and resid 329 through 349 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 316 Processing helix chain 'O' and resid 319 through 327 Processing helix chain 'O' and resid 329 through 349 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 316 Processing helix chain 'P' and resid 319 through 327 Processing helix chain 'P' and resid 329 through 349 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 316 Processing helix chain 'Q' and resid 319 through 327 Processing helix chain 'Q' and resid 329 through 349 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 316 Processing helix chain 'R' and resid 319 through 327 Processing helix chain 'R' and resid 329 through 349 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 316 Processing helix chain 'S' and resid 319 through 327 Processing helix chain 'S' and resid 329 through 349 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 316 Processing helix chain 'T' and resid 319 through 327 Processing helix chain 'T' and resid 329 through 349 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 316 Processing helix chain 'U' and resid 319 through 327 Processing helix chain 'U' and resid 329 through 349 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 316 Processing helix chain 'V' and resid 319 through 327 Processing helix chain 'V' and resid 329 through 349 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 316 Processing helix chain 'W' and resid 319 through 327 Processing helix chain 'W' and resid 329 through 349 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 316 Processing helix chain 'X' and resid 319 through 327 Processing helix chain 'X' and resid 329 through 349 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 316 Processing helix chain 'Y' and resid 319 through 327 Processing helix chain 'Y' and resid 329 through 349 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 316 Processing helix chain 'Z' and resid 319 through 327 Processing helix chain 'Z' and resid 329 through 349 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 316 Processing helix chain 'a' and resid 319 through 327 Processing helix chain 'a' and resid 329 through 349 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 316 Processing helix chain 'b' and resid 319 through 327 Processing helix chain 'b' and resid 329 through 349 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 316 Processing helix chain 'c' and resid 319 through 327 Processing helix chain 'c' and resid 329 through 349 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 316 Processing helix chain 'd' and resid 319 through 327 Processing helix chain 'd' and resid 329 through 349 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 316 Processing helix chain 'e' and resid 319 through 327 Processing helix chain 'e' and resid 329 through 349 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 316 Processing helix chain 'f' and resid 319 through 327 Processing helix chain 'f' and resid 329 through 349 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 316 Processing helix chain 'g' and resid 319 through 327 Processing helix chain 'g' and resid 329 through 349 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 316 Processing helix chain 'h' and resid 319 through 327 Processing helix chain 'h' and resid 329 through 349 1293 hydrogen bonds defined for protein. 3879 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: 2.03 Time building geometry restraints manager: 1.74 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: 6222 1.34 - 1.46: 3247 1.46 - 1.58: 8449 1.58 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 18020 Sorted by residual: bond pdb=" CA ALA I 327 " pdb=" CB ALA I 327 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.98e-02 2.55e+03 6.47e-01 bond pdb=" CA ALA b 327 " pdb=" CB ALA b 327 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.98e-02 2.55e+03 6.43e-01 bond pdb=" CA ALA C 327 " pdb=" CB ALA C 327 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.98e-02 2.55e+03 6.31e-01 bond pdb=" CA ALA Q 327 " pdb=" CB ALA Q 327 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.98e-02 2.55e+03 6.30e-01 bond pdb=" CA ALA h 327 " pdb=" CB ALA h 327 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.98e-02 2.55e+03 6.28e-01 ... (remaining 18015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 22170 1.05 - 2.10: 1522 2.10 - 3.15: 482 3.15 - 4.20: 68 4.20 - 5.25: 136 Bond angle restraints: 24378 Sorted by residual: angle pdb=" CA ARG Q 334 " pdb=" CB ARG Q 334 " pdb=" CG ARG Q 334 " ideal model delta sigma weight residual 114.10 118.72 -4.62 2.00e+00 2.50e-01 5.35e+00 angle pdb=" CA ARG F 334 " pdb=" CB ARG F 334 " pdb=" CG ARG F 334 " ideal model delta sigma weight residual 114.10 118.72 -4.62 2.00e+00 2.50e-01 5.34e+00 angle pdb=" CA ARG C 334 " pdb=" CB ARG C 334 " pdb=" CG ARG C 334 " ideal model delta sigma weight residual 114.10 118.72 -4.62 2.00e+00 2.50e-01 5.33e+00 angle pdb=" CA ARG V 334 " pdb=" CB ARG V 334 " pdb=" CG ARG V 334 " ideal model delta sigma weight residual 114.10 118.71 -4.61 2.00e+00 2.50e-01 5.31e+00 angle pdb=" CA ARG O 334 " pdb=" CB ARG O 334 " pdb=" CG ARG O 334 " ideal model delta sigma weight residual 114.10 118.70 -4.60 2.00e+00 2.50e-01 5.30e+00 ... (remaining 24373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.10: 9833 12.10 - 24.19: 843 24.19 - 36.29: 442 36.29 - 48.38: 34 48.38 - 60.48: 68 Dihedral angle restraints: 11220 sinusoidal: 4386 harmonic: 6834 Sorted by residual: dihedral pdb=" CA ARG Z 334 " pdb=" C ARG Z 334 " pdb=" N VAL Z 335 " pdb=" CA VAL Z 335 " ideal model delta harmonic sigma weight residual 180.00 166.01 13.99 0 5.00e+00 4.00e-02 7.83e+00 dihedral pdb=" CA ARG X 334 " pdb=" C ARG X 334 " pdb=" N VAL X 335 " pdb=" CA VAL X 335 " ideal model delta harmonic sigma weight residual 180.00 166.01 13.99 0 5.00e+00 4.00e-02 7.83e+00 dihedral pdb=" CA ARG d 334 " pdb=" C ARG d 334 " pdb=" N VAL d 335 " pdb=" CA VAL d 335 " ideal model delta harmonic sigma weight residual 180.00 166.01 13.99 0 5.00e+00 4.00e-02 7.83e+00 ... (remaining 11217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 1297 0.022 - 0.045: 967 0.045 - 0.067: 309 0.067 - 0.090: 208 0.090 - 0.112: 109 Chirality restraints: 2890 Sorted by residual: chirality pdb=" CA PHE f 349 " pdb=" N PHE f 349 " pdb=" C PHE f 349 " pdb=" CB PHE f 349 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.15e-01 chirality pdb=" CA PHE b 349 " pdb=" N PHE b 349 " pdb=" C PHE b 349 " pdb=" CB PHE b 349 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.13e-01 chirality pdb=" CA PHE g 349 " pdb=" N PHE g 349 " pdb=" C PHE g 349 " pdb=" CB PHE g 349 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.08e-01 ... (remaining 2887 not shown) Planarity restraints: 3230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG H 334 " -0.008 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C ARG H 334 " 0.026 2.00e-02 2.50e+03 pdb=" O ARG H 334 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL H 335 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 334 " -0.008 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C ARG C 334 " 0.026 2.00e-02 2.50e+03 pdb=" O ARG C 334 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C 335 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG g 334 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C ARG g 334 " 0.026 2.00e-02 2.50e+03 pdb=" O ARG g 334 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL g 335 " -0.009 2.00e-02 2.50e+03 ... (remaining 3227 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 85 2.55 - 3.14: 14320 3.14 - 3.73: 30620 3.73 - 4.31: 36252 4.31 - 4.90: 59251 Nonbonded interactions: 140528 Sorted by model distance: nonbonded pdb=" NH1 ARG P 334 " pdb=" O THR e 317 " model vdw 1.963 3.120 nonbonded pdb=" O THR Y 317 " pdb=" NH1 ARG a 334 " model vdw 2.021 3.120 nonbonded pdb=" O THR G 317 " pdb=" NH1 ARG I 334 " model vdw 2.057 3.120 nonbonded pdb=" O THR I 317 " pdb=" NH1 ARG K 334 " model vdw 2.060 3.120 nonbonded pdb=" NH1 ARG b 334 " pdb=" O THR d 317 " model vdw 2.060 3.120 ... (remaining 140523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } 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: 3.670 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: 0.050 Set scattering table: 0.040 Process input model: 11.030 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 18020 Z= 0.179 Angle : 0.727 5.254 24378 Z= 0.404 Chirality : 0.040 0.112 2890 Planarity : 0.005 0.026 3230 Dihedral : 12.641 60.480 6732 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: 1.55 (0.18), residues: 2278 helix: 1.31 (0.12), residues: 2074 sheet: None (None), residues: 0 loop : -1.44 (0.50), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 334 TYR 0.005 0.001 TYR O 284 PHE 0.022 0.004 PHE I 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (18020) covalent geometry : angle 0.72676 / 0.40 (24378) hydrogen bonds : bond 0.06572 / 4.45 ( 1293) hydrogen bonds : angle 4.21620 / 2.90 ( 3879) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 0.557 Fit side-chains REVERT: A 294 GLU cc_start: 0.7312 (tp30) cc_final: 0.7036 (tp30) REVERT: A 345 THR cc_start: 0.8433 (m) cc_final: 0.8219 (p) REVERT: B 345 THR cc_start: 0.8651 (m) cc_final: 0.8232 (p) REVERT: C 345 THR cc_start: 0.8613 (m) cc_final: 0.8277 (p) REVERT: E 314 VAL cc_start: 0.8702 (t) cc_final: 0.8478 (t) REVERT: F 342 SER cc_start: 0.8635 (t) cc_final: 0.8380 (t) REVERT: G 315 LEU cc_start: 0.8335 (tp) cc_final: 0.8096 (tp) REVERT: H 342 SER cc_start: 0.8333 (t) cc_final: 0.8114 (t) REVERT: H 345 THR cc_start: 0.8426 (m) cc_final: 0.8093 (p) REVERT: I 294 GLU cc_start: 0.7682 (tp30) cc_final: 0.7293 (tp30) REVERT: J 342 SER cc_start: 0.8665 (t) cc_final: 0.8441 (t) REVERT: J 345 THR cc_start: 0.8655 (m) cc_final: 0.8384 (p) REVERT: K 294 GLU cc_start: 0.7715 (tp30) cc_final: 0.7286 (tp30) REVERT: K 345 THR cc_start: 0.8542 (m) cc_final: 0.8143 (p) REVERT: M 345 THR cc_start: 0.8671 (m) cc_final: 0.8374 (p) REVERT: N 339 LEU cc_start: 0.8431 (tp) cc_final: 0.8212 (tt) REVERT: O 294 GLU cc_start: 0.7470 (tp30) cc_final: 0.7068 (tp30) REVERT: O 345 THR cc_start: 0.8644 (m) cc_final: 0.8249 (p) REVERT: P 294 GLU cc_start: 0.7684 (tp30) cc_final: 0.7123 (tp30) REVERT: Q 315 LEU cc_start: 0.8367 (tp) cc_final: 0.8167 (tp) REVERT: Q 345 THR cc_start: 0.8363 (m) cc_final: 0.8158 (p) REVERT: R 339 LEU cc_start: 0.8069 (tp) cc_final: 0.7822 (tt) REVERT: T 314 VAL cc_start: 0.8673 (t) cc_final: 0.8436 (p) REVERT: T 324 LYS cc_start: 0.8194 (mttp) cc_final: 0.7976 (mttp) REVERT: U 314 VAL cc_start: 0.8645 (t) cc_final: 0.8418 (t) REVERT: U 342 SER cc_start: 0.8443 (t) cc_final: 0.8197 (t) REVERT: U 345 THR cc_start: 0.8578 (m) cc_final: 0.8178 (p) REVERT: V 342 SER cc_start: 0.8703 (t) cc_final: 0.8494 (t) REVERT: V 345 THR cc_start: 0.8619 (m) cc_final: 0.8303 (t) REVERT: W 345 THR cc_start: 0.8483 (m) cc_final: 0.7985 (p) REVERT: X 314 VAL cc_start: 0.8388 (t) cc_final: 0.8089 (t) REVERT: X 317 THR cc_start: 0.8884 (m) cc_final: 0.8545 (p) REVERT: X 342 SER cc_start: 0.8427 (t) cc_final: 0.8176 (t) REVERT: X 345 THR cc_start: 0.8601 (m) cc_final: 0.8206 (p) REVERT: Y 294 GLU cc_start: 0.7634 (tp30) cc_final: 0.7203 (tp30) REVERT: Y 341 SER cc_start: 0.8130 (m) cc_final: 0.7799 (t) REVERT: Y 345 THR cc_start: 0.8293 (m) cc_final: 0.7992 (p) REVERT: Z 341 SER cc_start: 0.8270 (m) cc_final: 0.7975 (t) REVERT: Z 342 SER cc_start: 0.8492 (t) cc_final: 0.8172 (t) REVERT: Z 345 THR cc_start: 0.8536 (m) cc_final: 0.8091 (p) REVERT: a 294 GLU cc_start: 0.7733 (tp30) cc_final: 0.7495 (tp30) REVERT: a 317 THR cc_start: 0.8780 (m) cc_final: 0.8541 (p) REVERT: a 345 THR cc_start: 0.8572 (m) cc_final: 0.8239 (p) REVERT: b 294 GLU cc_start: 0.7682 (tp30) cc_final: 0.7357 (tp30) REVERT: b 342 SER cc_start: 0.8509 (t) cc_final: 0.8269 (t) REVERT: b 345 THR cc_start: 0.8751 (m) cc_final: 0.8297 (p) REVERT: c 345 THR cc_start: 0.8460 (m) cc_final: 0.8158 (p) REVERT: d 315 LEU cc_start: 0.8356 (tp) cc_final: 0.8119 (tp) REVERT: d 318 LEU cc_start: 0.8682 (mm) cc_final: 0.8465 (mm) REVERT: d 345 THR cc_start: 0.8435 (m) cc_final: 0.8205 (p) REVERT: e 317 THR cc_start: 0.8727 (m) cc_final: 0.8364 (t) REVERT: e 341 SER cc_start: 0.8127 (m) cc_final: 0.7831 (t) REVERT: e 342 SER cc_start: 0.8356 (t) cc_final: 0.8089 (t) REVERT: e 345 THR cc_start: 0.8236 (m) cc_final: 0.7954 (p) REVERT: f 294 GLU cc_start: 0.7648 (tp30) cc_final: 0.7243 (tp30) REVERT: h 314 VAL cc_start: 0.8557 (t) cc_final: 0.8192 (p) outliers start: 0 outliers final: 0 residues processed: 530 average time/residue: 0.0995 time to fit residues: 85.4980 Evaluate side-chains 484 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 484 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 307 GLN J 307 GLN S 307 GLN d 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.168230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149531 restraints weight = 27475.792| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 3.07 r_work: 0.3839 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18020 Z= 0.149 Angle : 0.665 10.461 24378 Z= 0.310 Chirality : 0.039 0.251 2890 Planarity : 0.005 0.040 3230 Dihedral : 4.350 13.208 2550 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.76 % Allowed : 11.82 % Favored : 87.42 % 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: 1.79 (0.18), residues: 2278 helix: 1.46 (0.12), residues: 2074 sheet: None (None), residues: 0 loop : -1.29 (0.52), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 334 TYR 0.005 0.001 TYR V 284 PHE 0.015 0.002 PHE Y 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (18020) covalent geometry : angle 0.66461 / 0.31 (24378) hydrogen bonds : bond 0.03694 / 2.48 ( 1293) hydrogen bonds : angle 3.53069 / 2.43 ( 3879) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 499 time to evaluate : 0.494 Fit side-chains REVERT: C 288 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7379 (mm) REVERT: E 347 MET cc_start: 0.8177 (tpp) cc_final: 0.7916 (mmm) REVERT: H 347 MET cc_start: 0.8240 (tpp) cc_final: 0.7997 (tpp) REVERT: I 294 GLU cc_start: 0.7812 (tp30) cc_final: 0.7518 (tp30) REVERT: J 345 THR cc_start: 0.8733 (m) cc_final: 0.8419 (p) REVERT: L 317 THR cc_start: 0.9185 (m) cc_final: 0.8888 (p) REVERT: L 345 THR cc_start: 0.8562 (m) cc_final: 0.8319 (p) REVERT: L 347 MET cc_start: 0.8725 (tpp) cc_final: 0.8390 (tpp) REVERT: M 342 SER cc_start: 0.8980 (t) cc_final: 0.8657 (t) REVERT: M 345 THR cc_start: 0.8903 (m) cc_final: 0.8448 (p) REVERT: N 339 LEU cc_start: 0.8644 (tp) cc_final: 0.8412 (tt) REVERT: O 312 PRO cc_start: 0.8939 (Cg_exo) cc_final: 0.8727 (Cg_endo) REVERT: Q 345 THR cc_start: 0.8629 (m) cc_final: 0.8383 (p) REVERT: R 339 LEU cc_start: 0.8318 (tp) cc_final: 0.8074 (tt) REVERT: S 347 MET cc_start: 0.8141 (tpp) cc_final: 0.7475 (mpp) REVERT: T 324 LYS cc_start: 0.8343 (mttp) cc_final: 0.8112 (mttp) REVERT: V 342 SER cc_start: 0.8999 (t) cc_final: 0.8526 (p) REVERT: V 345 THR cc_start: 0.8652 (m) cc_final: 0.8405 (t) REVERT: V 347 MET cc_start: 0.8442 (tpp) cc_final: 0.8008 (tpp) REVERT: X 314 VAL cc_start: 0.8510 (t) cc_final: 0.8259 (t) REVERT: X 317 THR cc_start: 0.9036 (m) cc_final: 0.8799 (p) REVERT: X 342 SER cc_start: 0.8818 (t) cc_final: 0.8496 (p) REVERT: Z 318 LEU cc_start: 0.8758 (mm) cc_final: 0.8527 (mp) REVERT: a 294 GLU cc_start: 0.7864 (tp30) cc_final: 0.7565 (tp30) REVERT: a 317 THR cc_start: 0.8968 (m) cc_final: 0.8725 (p) REVERT: b 294 GLU cc_start: 0.7824 (tp30) cc_final: 0.7570 (tp30) REVERT: b 347 MET cc_start: 0.8334 (tpp) cc_final: 0.7414 (mpp) REVERT: b 348 GLN cc_start: 0.8660 (mt0) cc_final: 0.8403 (mt0) REVERT: d 345 THR cc_start: 0.8665 (m) cc_final: 0.8444 (p) REVERT: e 318 LEU cc_start: 0.8964 (mm) cc_final: 0.8739 (mp) REVERT: e 341 SER cc_start: 0.8542 (m) cc_final: 0.8228 (t) REVERT: e 345 THR cc_start: 0.8461 (m) cc_final: 0.8113 (p) REVERT: f 347 MET cc_start: 0.8113 (tpp) cc_final: 0.7056 (mpp) REVERT: g 347 MET cc_start: 0.8069 (tpp) cc_final: 0.7747 (tpp) REVERT: h 288 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7466 (mm) outliers start: 14 outliers final: 8 residues processed: 503 average time/residue: 0.0934 time to fit residues: 76.6960 Evaluate side-chains 500 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 490 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain P residue 324 LYS Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 342 SER Chi-restraints excluded: chain h residue 288 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 154 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 307 GLN N 307 GLN S 307 GLN Z 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.166461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.148005 restraints weight = 27507.730| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.96 r_work: 0.3825 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18020 Z= 0.152 Angle : 0.631 11.402 24378 Z= 0.290 Chirality : 0.039 0.130 2890 Planarity : 0.005 0.046 3230 Dihedral : 4.045 12.816 2550 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.42 % Allowed : 18.36 % Favored : 80.23 % 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 (0.18), residues: 2278 helix: 1.47 (0.11), residues: 2074 sheet: None (None), residues: 0 loop : -1.15 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.006 0.001 TYR e 284 PHE 0.014 0.002 PHE G 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (18020) covalent geometry : angle 0.63065 / 0.29 (24378) hydrogen bonds : bond 0.03569 / 2.40 ( 1293) hydrogen bonds : angle 3.41655 / 2.34 ( 3879) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 517 time to evaluate : 0.633 Fit side-chains REVERT: C 288 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7418 (mm) REVERT: F 348 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7979 (mp10) REVERT: G 347 MET cc_start: 0.8326 (tpp) cc_final: 0.7848 (mmm) REVERT: H 347 MET cc_start: 0.8245 (tpp) cc_final: 0.8031 (tpp) REVERT: I 294 GLU cc_start: 0.7819 (tp30) cc_final: 0.7558 (tp30) REVERT: J 345 THR cc_start: 0.8784 (m) cc_final: 0.8418 (p) REVERT: K 347 MET cc_start: 0.8433 (tpp) cc_final: 0.7972 (tpp) REVERT: L 317 THR cc_start: 0.9143 (m) cc_final: 0.8871 (p) REVERT: L 347 MET cc_start: 0.8638 (tpp) cc_final: 0.8389 (tpp) REVERT: O 294 GLU cc_start: 0.7731 (tp30) cc_final: 0.7444 (tp30) REVERT: O 352 GLN cc_start: 0.8986 (mp10) cc_final: 0.8655 (mp10) REVERT: Q 345 THR cc_start: 0.8727 (m) cc_final: 0.8449 (p) REVERT: R 294 GLU cc_start: 0.8024 (tp30) cc_final: 0.7556 (tp30) REVERT: R 339 LEU cc_start: 0.8365 (tp) cc_final: 0.8085 (tt) REVERT: R 348 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7941 (mm-40) REVERT: S 347 MET cc_start: 0.8132 (tpp) cc_final: 0.7611 (mpp) REVERT: T 324 LYS cc_start: 0.8265 (mttp) cc_final: 0.8058 (mttp) REVERT: T 345 THR cc_start: 0.8740 (t) cc_final: 0.8422 (p) REVERT: V 330 LEU cc_start: 0.7660 (tt) cc_final: 0.7458 (tp) REVERT: V 342 SER cc_start: 0.8983 (t) cc_final: 0.8708 (p) REVERT: X 317 THR cc_start: 0.9100 (m) cc_final: 0.8874 (p) REVERT: X 342 SER cc_start: 0.8813 (t) cc_final: 0.8471 (p) REVERT: Y 305 LEU cc_start: 0.8442 (mm) cc_final: 0.8237 (mp) REVERT: a 294 GLU cc_start: 0.7845 (tp30) cc_final: 0.7585 (tp30) REVERT: a 305 LEU cc_start: 0.8404 (mm) cc_final: 0.8194 (mp) REVERT: b 347 MET cc_start: 0.8272 (tpp) cc_final: 0.7420 (mpp) REVERT: b 348 GLN cc_start: 0.8568 (mt0) cc_final: 0.8307 (mt0) REVERT: d 345 THR cc_start: 0.8669 (m) cc_final: 0.8451 (p) REVERT: e 341 SER cc_start: 0.8591 (m) cc_final: 0.8285 (t) REVERT: e 345 THR cc_start: 0.8498 (m) cc_final: 0.8117 (p) REVERT: f 347 MET cc_start: 0.8146 (tpp) cc_final: 0.7205 (mpp) REVERT: h 288 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7455 (mm) outliers start: 26 outliers final: 16 residues processed: 522 average time/residue: 0.0970 time to fit residues: 82.2809 Evaluate side-chains 527 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 509 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 342 SER Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain P residue 324 LYS Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain S residue 348 GLN Chi-restraints excluded: chain X residue 291 LEU Chi-restraints excluded: chain X residue 349 PHE Chi-restraints excluded: chain Y residue 324 LYS Chi-restraints excluded: chain Z residue 341 SER Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 342 SER Chi-restraints excluded: chain c residue 324 LYS Chi-restraints excluded: chain h residue 288 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 152 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 307 GLN S 307 GLN Y 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.164699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.145445 restraints weight = 27193.942| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 3.05 r_work: 0.3778 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18020 Z= 0.207 Angle : 0.664 11.949 24378 Z= 0.307 Chirality : 0.043 0.324 2890 Planarity : 0.005 0.049 3230 Dihedral : 4.135 14.192 2550 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.53 % Allowed : 22.28 % Favored : 76.20 % 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: 1.56 (0.18), residues: 2278 helix: 1.27 (0.11), residues: 2074 sheet: None (None), residues: 0 loop : -0.84 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 351 TYR 0.006 0.001 TYR b 284 PHE 0.020 0.003 PHE F 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (18020) covalent geometry : angle 0.66385 / 0.31 (24378) hydrogen bonds : bond 0.03845 / 2.58 ( 1293) hydrogen bonds : angle 3.63105 / 2.49 ( 3879) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 522 time to evaluate : 0.680 Fit side-chains REVERT: C 288 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7485 (mm) REVERT: F 348 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8091 (mp10) REVERT: H 347 MET cc_start: 0.8375 (tpp) cc_final: 0.8078 (tpp) REVERT: K 347 MET cc_start: 0.8499 (tpp) cc_final: 0.8100 (tpp) REVERT: L 317 THR cc_start: 0.9215 (m) cc_final: 0.8993 (p) REVERT: L 324 LYS cc_start: 0.8447 (mttp) cc_final: 0.8223 (mttp) REVERT: L 347 MET cc_start: 0.8678 (tpp) cc_final: 0.8449 (tpp) REVERT: M 348 GLN cc_start: 0.8624 (mt0) cc_final: 0.8323 (mt0) REVERT: O 294 GLU cc_start: 0.7837 (tp30) cc_final: 0.7497 (tp30) REVERT: O 352 GLN cc_start: 0.8968 (mp10) cc_final: 0.8746 (mp10) REVERT: Q 345 THR cc_start: 0.8734 (m) cc_final: 0.8437 (p) REVERT: Q 347 MET cc_start: 0.8244 (tpp) cc_final: 0.7704 (mpp) REVERT: R 294 GLU cc_start: 0.8104 (tp30) cc_final: 0.7657 (tp30) REVERT: R 339 LEU cc_start: 0.8327 (tp) cc_final: 0.8047 (tt) REVERT: R 347 MET cc_start: 0.8221 (tpp) cc_final: 0.7685 (tpp) REVERT: R 348 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7971 (mp10) REVERT: S 347 MET cc_start: 0.8186 (tpp) cc_final: 0.7697 (mpp) REVERT: T 324 LYS cc_start: 0.8317 (mttp) cc_final: 0.8107 (mttp) REVERT: T 345 THR cc_start: 0.8738 (t) cc_final: 0.8406 (p) REVERT: V 330 LEU cc_start: 0.7731 (tt) cc_final: 0.7507 (tp) REVERT: V 347 MET cc_start: 0.8328 (tpp) cc_final: 0.7759 (tpp) REVERT: X 317 THR cc_start: 0.9177 (m) cc_final: 0.8956 (p) REVERT: X 342 SER cc_start: 0.8744 (t) cc_final: 0.8398 (p) REVERT: Y 334 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7854 (ttm-80) REVERT: b 294 GLU cc_start: 0.7965 (tp30) cc_final: 0.7571 (tp30) REVERT: b 347 MET cc_start: 0.8278 (tpp) cc_final: 0.7476 (mpp) REVERT: c 334 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7946 (ttm170) REVERT: c 347 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8192 (mmm) REVERT: d 345 THR cc_start: 0.8654 (m) cc_final: 0.8422 (p) REVERT: e 345 THR cc_start: 0.8487 (m) cc_final: 0.8094 (p) REVERT: f 347 MET cc_start: 0.8215 (tpp) cc_final: 0.7335 (mpp) REVERT: h 288 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7454 (mm) outliers start: 28 outliers final: 18 residues processed: 530 average time/residue: 0.0965 time to fit residues: 82.3781 Evaluate side-chains 536 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 515 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 342 SER Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain N residue 342 SER Chi-restraints excluded: chain P residue 324 LYS Chi-restraints excluded: chain S residue 348 GLN Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain W residue 342 SER Chi-restraints excluded: chain X residue 291 LEU Chi-restraints excluded: chain Y residue 324 LYS Chi-restraints excluded: chain Z residue 341 SER Chi-restraints excluded: chain Z residue 342 SER Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 342 SER Chi-restraints excluded: chain b residue 342 SER Chi-restraints excluded: chain c residue 347 MET Chi-restraints excluded: chain d residue 324 LYS Chi-restraints excluded: chain h residue 288 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 153 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 307 GLN I 307 GLN S 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.166424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.147599 restraints weight = 27319.376| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.98 r_work: 0.3818 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18020 Z= 0.141 Angle : 0.676 13.285 24378 Z= 0.295 Chirality : 0.040 0.351 2890 Planarity : 0.005 0.044 3230 Dihedral : 3.966 16.054 2550 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.74 % Allowed : 25.00 % Favored : 73.26 % 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: 1.80 (0.18), residues: 2278 helix: 1.41 (0.11), residues: 2074 sheet: None (None), residues: 0 loop : -0.56 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 334 TYR 0.005 0.001 TYR Y 284 PHE 0.020 0.002 PHE J 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (18020) covalent geometry : angle 0.67604 / 0.29 (24378) hydrogen bonds : bond 0.03329 / 2.23 ( 1293) hydrogen bonds : angle 3.53369 / 2.43 ( 3879) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 508 time to evaluate : 0.570 Fit side-chains REVERT: B 347 MET cc_start: 0.8156 (tpp) cc_final: 0.7868 (tpp) REVERT: C 288 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7436 (mm) REVERT: E 347 MET cc_start: 0.8182 (tpp) cc_final: 0.7519 (mpp) REVERT: F 294 GLU cc_start: 0.8102 (tp30) cc_final: 0.7770 (tp30) REVERT: F 348 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8115 (mp10) REVERT: H 347 MET cc_start: 0.8304 (tpp) cc_final: 0.8040 (tpp) REVERT: J 314 VAL cc_start: 0.8766 (t) cc_final: 0.8550 (t) REVERT: J 317 THR cc_start: 0.8937 (m) cc_final: 0.8683 (p) REVERT: J 345 THR cc_start: 0.8789 (m) cc_final: 0.8371 (p) REVERT: K 347 MET cc_start: 0.8437 (tpp) cc_final: 0.8041 (tpp) REVERT: L 317 THR cc_start: 0.9082 (m) cc_final: 0.8854 (p) REVERT: L 324 LYS cc_start: 0.8409 (mttp) cc_final: 0.8177 (mttp) REVERT: N 347 MET cc_start: 0.8406 (mmm) cc_final: 0.8168 (mmm) REVERT: O 294 GLU cc_start: 0.7685 (tp30) cc_final: 0.7400 (tp30) REVERT: Q 307 GLN cc_start: 0.8049 (mt0) cc_final: 0.7815 (mt0) REVERT: Q 345 THR cc_start: 0.8817 (m) cc_final: 0.8509 (p) REVERT: Q 347 MET cc_start: 0.8269 (tpp) cc_final: 0.7647 (mpp) REVERT: R 294 GLU cc_start: 0.8040 (tp30) cc_final: 0.7556 (tp30) REVERT: R 339 LEU cc_start: 0.8342 (tp) cc_final: 0.8077 (tt) REVERT: S 347 MET cc_start: 0.8162 (tpp) cc_final: 0.7851 (mpp) REVERT: T 345 THR cc_start: 0.8784 (t) cc_final: 0.8455 (p) REVERT: T 347 MET cc_start: 0.8326 (tpp) cc_final: 0.7876 (tpp) REVERT: V 330 LEU cc_start: 0.7654 (tt) cc_final: 0.7433 (tp) REVERT: V 347 MET cc_start: 0.8320 (tpp) cc_final: 0.7813 (tpp) REVERT: X 294 GLU cc_start: 0.7827 (tp30) cc_final: 0.7555 (tp30) REVERT: X 317 THR cc_start: 0.9180 (m) cc_final: 0.8949 (p) REVERT: X 342 SER cc_start: 0.8779 (t) cc_final: 0.8434 (p) REVERT: Y 318 LEU cc_start: 0.8966 (mm) cc_final: 0.8733 (mp) REVERT: Y 334 ARG cc_start: 0.8021 (ttm170) cc_final: 0.7528 (mtt-85) REVERT: Z 305 LEU cc_start: 0.8379 (mm) cc_final: 0.8174 (mp) REVERT: a 305 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8225 (mp) REVERT: b 294 GLU cc_start: 0.7895 (tp30) cc_final: 0.7548 (tp30) REVERT: c 347 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8186 (mmm) REVERT: d 345 THR cc_start: 0.8673 (m) cc_final: 0.8450 (p) REVERT: e 318 LEU cc_start: 0.9081 (mm) cc_final: 0.8821 (mp) REVERT: e 345 THR cc_start: 0.8458 (m) cc_final: 0.8083 (p) REVERT: f 347 MET cc_start: 0.8185 (tpp) cc_final: 0.7400 (mpp) REVERT: h 288 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7485 (mm) outliers start: 32 outliers final: 21 residues processed: 519 average time/residue: 0.0982 time to fit residues: 82.7213 Evaluate side-chains 529 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 504 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain I residue 349 PHE Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain M residue 342 SER Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain S residue 348 GLN Chi-restraints excluded: chain V residue 324 LYS Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain V residue 349 PHE Chi-restraints excluded: chain W residue 342 SER Chi-restraints excluded: chain X residue 291 LEU Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain Z residue 341 SER Chi-restraints excluded: chain Z residue 342 SER Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 305 LEU Chi-restraints excluded: chain a residue 342 SER Chi-restraints excluded: chain b residue 342 SER Chi-restraints excluded: chain c residue 347 MET Chi-restraints excluded: chain f residue 342 SER Chi-restraints excluded: chain h residue 288 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 139 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 130 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 197 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 153 optimal weight: 0.0970 chunk 150 optimal weight: 6.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 307 GLN N 307 GLN S 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.168434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.149772 restraints weight = 27152.962| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.96 r_work: 0.3844 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18020 Z= 0.118 Angle : 0.685 13.567 24378 Z= 0.292 Chirality : 0.039 0.301 2890 Planarity : 0.005 0.044 3230 Dihedral : 3.835 19.125 2550 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.61 % Allowed : 26.20 % Favored : 71.19 % 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: 2.06 (0.18), residues: 2278 helix: 1.58 (0.11), residues: 2074 sheet: None (None), residues: 0 loop : -0.53 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 334 TYR 0.004 0.001 TYR Q 284 PHE 0.020 0.002 PHE V 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (18020) covalent geometry : angle 0.68539 / 0.29 (24378) hydrogen bonds : bond 0.03053 / 2.04 ( 1293) hydrogen bonds : angle 3.51224 / 2.40 ( 3879) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 505 time to evaluate : 0.415 Fit side-chains REVERT: B 347 MET cc_start: 0.8113 (tpp) cc_final: 0.7756 (tpp) REVERT: D 347 MET cc_start: 0.7984 (tpp) cc_final: 0.7655 (tpp) REVERT: E 347 MET cc_start: 0.8191 (tpp) cc_final: 0.7550 (mpp) REVERT: F 294 GLU cc_start: 0.8023 (tp30) cc_final: 0.7698 (tp30) REVERT: F 348 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8150 (mm-40) REVERT: G 347 MET cc_start: 0.8247 (mmm) cc_final: 0.8044 (mmm) REVERT: H 347 MET cc_start: 0.8234 (tpp) cc_final: 0.7984 (tpp) REVERT: J 317 THR cc_start: 0.8878 (m) cc_final: 0.8639 (p) REVERT: K 347 MET cc_start: 0.8352 (tpp) cc_final: 0.7936 (tpp) REVERT: L 317 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8848 (p) REVERT: L 324 LYS cc_start: 0.8391 (mttp) cc_final: 0.8175 (mttp) REVERT: L 347 MET cc_start: 0.8571 (tpp) cc_final: 0.8002 (tpp) REVERT: O 294 GLU cc_start: 0.7656 (tp30) cc_final: 0.7360 (tp30) REVERT: Q 307 GLN cc_start: 0.7990 (mt0) cc_final: 0.7750 (mt0) REVERT: Q 345 THR cc_start: 0.8796 (m) cc_final: 0.8506 (p) REVERT: Q 347 MET cc_start: 0.8215 (tpp) cc_final: 0.7512 (mpp) REVERT: R 339 LEU cc_start: 0.8316 (tp) cc_final: 0.8070 (tt) REVERT: S 347 MET cc_start: 0.8141 (tpp) cc_final: 0.7844 (mpp) REVERT: T 345 THR cc_start: 0.8780 (t) cc_final: 0.8450 (p) REVERT: T 347 MET cc_start: 0.8264 (tpp) cc_final: 0.7848 (tpp) REVERT: V 330 LEU cc_start: 0.7628 (tt) cc_final: 0.7411 (tp) REVERT: V 347 MET cc_start: 0.8271 (tpp) cc_final: 0.7663 (tpp) REVERT: W 294 GLU cc_start: 0.7656 (tp30) cc_final: 0.7400 (tp30) REVERT: X 294 GLU cc_start: 0.7763 (tp30) cc_final: 0.7487 (tp30) REVERT: X 317 THR cc_start: 0.9171 (m) cc_final: 0.8896 (p) REVERT: X 342 SER cc_start: 0.8717 (t) cc_final: 0.8385 (p) REVERT: Y 334 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7476 (mtt-85) REVERT: Z 341 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8595 (t) REVERT: b 294 GLU cc_start: 0.7864 (tp30) cc_final: 0.7543 (tp30) REVERT: c 347 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8150 (mmm) REVERT: d 345 THR cc_start: 0.8776 (m) cc_final: 0.8493 (p) REVERT: f 347 MET cc_start: 0.8138 (tpp) cc_final: 0.7573 (mpp) REVERT: h 288 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7454 (mm) outliers start: 48 outliers final: 22 residues processed: 523 average time/residue: 0.0886 time to fit residues: 75.7678 Evaluate side-chains 526 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 500 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 342 SER Chi-restraints excluded: chain J residue 349 PHE Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain M residue 342 SER Chi-restraints excluded: chain N residue 342 SER Chi-restraints excluded: chain O residue 341 SER Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain S residue 348 GLN Chi-restraints excluded: chain V residue 324 LYS Chi-restraints excluded: chain V residue 342 SER Chi-restraints excluded: chain V residue 349 PHE Chi-restraints excluded: chain W residue 342 SER Chi-restraints excluded: chain X residue 291 LEU Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain Z residue 339 LEU Chi-restraints excluded: chain Z residue 341 SER Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 342 SER Chi-restraints excluded: chain b residue 342 SER Chi-restraints excluded: chain c residue 347 MET Chi-restraints excluded: chain f residue 342 SER Chi-restraints excluded: chain h residue 288 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 27 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 118 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 307 GLN S 307 GLN U 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.149546 restraints weight = 27338.229| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 3.00 r_work: 0.3840 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18020 Z= 0.125 Angle : 0.735 14.953 24378 Z= 0.305 Chirality : 0.039 0.221 2890 Planarity : 0.005 0.042 3230 Dihedral : 3.823 18.184 2550 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.18 % Allowed : 27.89 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.07 (0.18), residues: 2278 helix: 1.60 (0.11), residues: 2074 sheet: None (None), residues: 0 loop : -0.65 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 334 TYR 0.005 0.001 TYR b 284 PHE 0.022 0.002 PHE V 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (18020) covalent geometry : angle 0.73455 / 0.30 (24378) hydrogen bonds : bond 0.03121 / 2.09 ( 1293) hydrogen bonds : angle 3.57293 / 2.44 ( 3879) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 504 time to evaluate : 0.616 Fit side-chains REVERT: B 347 MET cc_start: 0.8095 (tpp) cc_final: 0.7728 (tpp) REVERT: C 288 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7415 (mm) REVERT: D 347 MET cc_start: 0.8084 (tpp) cc_final: 0.7749 (tpp) REVERT: E 347 MET cc_start: 0.8177 (tpp) cc_final: 0.7575 (mpp) REVERT: F 294 GLU cc_start: 0.8006 (tp30) cc_final: 0.7695 (tp30) REVERT: F 348 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8161 (mm-40) REVERT: G 347 MET cc_start: 0.8241 (mmm) cc_final: 0.8004 (mmm) REVERT: H 347 MET cc_start: 0.8242 (tpp) cc_final: 0.8000 (tpp) REVERT: H 352 GLN cc_start: 0.8943 (mp10) cc_final: 0.8617 (mp10) REVERT: I 294 GLU cc_start: 0.7738 (tp30) cc_final: 0.7426 (tp30) REVERT: J 317 THR cc_start: 0.8937 (m) cc_final: 0.8697 (p) REVERT: J 345 THR cc_start: 0.8735 (m) cc_final: 0.8308 (p) REVERT: K 347 MET cc_start: 0.8341 (tpp) cc_final: 0.7924 (tpp) REVERT: L 317 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8856 (p) REVERT: L 324 LYS cc_start: 0.8380 (mttp) cc_final: 0.8177 (mttp) REVERT: L 347 MET cc_start: 0.8592 (tpp) cc_final: 0.8043 (tpp) REVERT: O 294 GLU cc_start: 0.7660 (tp30) cc_final: 0.7374 (tp30) REVERT: O 349 PHE cc_start: 0.7645 (m-80) cc_final: 0.7413 (t80) REVERT: Q 307 GLN cc_start: 0.7958 (mt0) cc_final: 0.7725 (mt0) REVERT: Q 345 THR cc_start: 0.8796 (m) cc_final: 0.8506 (p) REVERT: Q 347 MET cc_start: 0.8220 (tpp) cc_final: 0.7510 (mpp) REVERT: R 339 LEU cc_start: 0.8310 (tp) cc_final: 0.8067 (tt) REVERT: R 347 MET cc_start: 0.7971 (tpp) cc_final: 0.7720 (tpp) REVERT: S 294 GLU cc_start: 0.7699 (tp30) cc_final: 0.7118 (tp30) REVERT: T 345 THR cc_start: 0.8796 (t) cc_final: 0.8476 (p) REVERT: T 347 MET cc_start: 0.8256 (tpp) cc_final: 0.7855 (tpp) REVERT: V 347 MET cc_start: 0.8265 (tpp) cc_final: 0.7670 (tpp) REVERT: W 294 GLU cc_start: 0.7675 (tp30) cc_final: 0.7351 (tp30) REVERT: X 294 GLU cc_start: 0.7761 (tp30) cc_final: 0.7481 (tp30) REVERT: X 317 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8888 (p) REVERT: X 342 SER cc_start: 0.8765 (t) cc_final: 0.8432 (p) REVERT: Y 318 LEU cc_start: 0.9034 (mm) cc_final: 0.8733 (mp) REVERT: Y 334 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7452 (mtt-85) REVERT: Z 341 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8591 (t) REVERT: b 294 GLU cc_start: 0.7800 (tp30) cc_final: 0.7395 (tp30) REVERT: c 334 ARG cc_start: 0.8040 (ttm170) cc_final: 0.7829 (ttm-80) REVERT: c 347 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8116 (mmm) REVERT: d 345 THR cc_start: 0.8752 (m) cc_final: 0.8473 (p) REVERT: h 288 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7467 (mm) outliers start: 40 outliers final: 23 residues processed: 517 average time/residue: 0.0929 time to fit residues: 79.1006 Evaluate side-chains 530 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 501 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 342 SER Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain M residue 342 SER Chi-restraints excluded: chain N residue 342 SER Chi-restraints excluded: chain Q residue 348 GLN Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain S residue 348 GLN Chi-restraints excluded: chain V residue 324 LYS Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain V residue 342 SER Chi-restraints excluded: chain W residue 342 SER Chi-restraints excluded: chain W residue 348 GLN Chi-restraints excluded: chain X residue 291 LEU Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain Z residue 341 SER Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain b residue 342 SER Chi-restraints excluded: chain c residue 347 MET Chi-restraints excluded: chain f residue 342 SER Chi-restraints excluded: chain h residue 288 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 48 optimal weight: 6.9990 chunk 193 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 200 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 307 GLN U 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.167032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.148006 restraints weight = 27270.847| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.99 r_work: 0.3822 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18020 Z= 0.144 Angle : 0.765 14.765 24378 Z= 0.316 Chirality : 0.041 0.288 2890 Planarity : 0.005 0.043 3230 Dihedral : 3.879 15.909 2550 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.72 % Allowed : 27.72 % Favored : 69.55 % 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 (0.18), residues: 2278 helix: 1.55 (0.12), residues: 2074 sheet: None (None), residues: 0 loop : -0.87 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 351 TYR 0.004 0.001 TYR K 284 PHE 0.018 0.002 PHE V 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (18020) covalent geometry : angle 0.76494 / 0.32 (24378) hydrogen bonds : bond 0.03300 / 2.21 ( 1293) hydrogen bonds : angle 3.67100 / 2.51 ( 3879) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 511 time to evaluate : 0.619 Fit side-chains REVERT: A 307 GLN cc_start: 0.7892 (mt0) cc_final: 0.7650 (mt0) REVERT: B 347 MET cc_start: 0.8128 (tpp) cc_final: 0.7724 (tpp) REVERT: C 288 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7442 (mm) REVERT: D 347 MET cc_start: 0.8163 (tpp) cc_final: 0.7804 (tpp) REVERT: E 347 MET cc_start: 0.8197 (tpp) cc_final: 0.7629 (mpp) REVERT: F 294 GLU cc_start: 0.7998 (tp30) cc_final: 0.7690 (tp30) REVERT: F 348 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8192 (mm-40) REVERT: G 347 MET cc_start: 0.8263 (mmm) cc_final: 0.8007 (mmm) REVERT: H 347 MET cc_start: 0.8346 (tpp) cc_final: 0.8072 (tpp) REVERT: I 294 GLU cc_start: 0.7801 (tp30) cc_final: 0.7478 (tp30) REVERT: J 317 THR cc_start: 0.8948 (m) cc_final: 0.8719 (p) REVERT: J 345 THR cc_start: 0.8693 (m) cc_final: 0.8268 (p) REVERT: K 347 MET cc_start: 0.8359 (tpp) cc_final: 0.7946 (tpp) REVERT: L 317 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8867 (p) REVERT: L 324 LYS cc_start: 0.8389 (mttp) cc_final: 0.8180 (mttp) REVERT: L 347 MET cc_start: 0.8569 (tpp) cc_final: 0.8156 (tpp) REVERT: N 347 MET cc_start: 0.8441 (mmm) cc_final: 0.8238 (mmm) REVERT: O 294 GLU cc_start: 0.7672 (tp30) cc_final: 0.7358 (tp30) REVERT: Q 345 THR cc_start: 0.8807 (m) cc_final: 0.8512 (p) REVERT: Q 347 MET cc_start: 0.8276 (tpp) cc_final: 0.7604 (mpp) REVERT: R 294 GLU cc_start: 0.7947 (tp30) cc_final: 0.7458 (tp30) REVERT: R 339 LEU cc_start: 0.8314 (tp) cc_final: 0.8049 (tt) REVERT: R 347 MET cc_start: 0.8060 (tpp) cc_final: 0.7678 (tpp) REVERT: S 294 GLU cc_start: 0.7743 (tp30) cc_final: 0.7165 (tp30) REVERT: T 345 THR cc_start: 0.8802 (t) cc_final: 0.8483 (p) REVERT: T 347 MET cc_start: 0.8270 (tpp) cc_final: 0.7833 (tpp) REVERT: V 347 MET cc_start: 0.8299 (tpp) cc_final: 0.7705 (tpp) REVERT: W 294 GLU cc_start: 0.7683 (tp30) cc_final: 0.7346 (tp30) REVERT: X 294 GLU cc_start: 0.7765 (tp30) cc_final: 0.7490 (tp30) REVERT: X 342 SER cc_start: 0.8767 (t) cc_final: 0.8422 (p) REVERT: Y 318 LEU cc_start: 0.9045 (mm) cc_final: 0.8739 (mp) REVERT: Z 294 GLU cc_start: 0.7738 (tp30) cc_final: 0.7481 (tp30) REVERT: b 294 GLU cc_start: 0.7790 (tp30) cc_final: 0.7402 (tp30) REVERT: c 334 ARG cc_start: 0.8075 (ttm170) cc_final: 0.7868 (tpp80) REVERT: c 347 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8132 (mmm) REVERT: d 345 THR cc_start: 0.8778 (m) cc_final: 0.8497 (p) REVERT: h 288 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7513 (mm) outliers start: 50 outliers final: 26 residues processed: 530 average time/residue: 0.1000 time to fit residues: 84.8875 Evaluate side-chains 528 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 498 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 342 SER Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain M residue 342 SER Chi-restraints excluded: chain N residue 342 SER Chi-restraints excluded: chain Q residue 348 GLN Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain S residue 348 GLN Chi-restraints excluded: chain V residue 324 LYS Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain V residue 342 SER Chi-restraints excluded: chain X residue 291 LEU Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain Z residue 341 SER Chi-restraints excluded: chain Z residue 342 SER Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 342 SER Chi-restraints excluded: chain b residue 342 SER Chi-restraints excluded: chain c residue 347 MET Chi-restraints excluded: chain f residue 342 SER Chi-restraints excluded: chain h residue 288 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 16 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 307 GLN U 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.162996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.143957 restraints weight = 27143.643| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.96 r_work: 0.3765 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18020 Z= 0.241 Angle : 0.824 14.802 24378 Z= 0.354 Chirality : 0.046 0.408 2890 Planarity : 0.005 0.049 3230 Dihedral : 4.232 19.140 2550 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.18 % Allowed : 28.16 % Favored : 69.66 % 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: 1.59 (0.18), residues: 2278 helix: 1.29 (0.12), residues: 2074 sheet: None (None), residues: 0 loop : -0.82 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 334 TYR 0.007 0.001 TYR b 284 PHE 0.023 0.003 PHE M 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.24 (18020) covalent geometry : angle 0.82356 / 0.35 (24378) hydrogen bonds : bond 0.03999 / 2.67 ( 1293) hydrogen bonds : angle 3.90747 / 2.68 ( 3879) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 530 time to evaluate : 0.677 Fit side-chains REVERT: B 347 MET cc_start: 0.8213 (tpp) cc_final: 0.7736 (tpp) REVERT: C 288 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7481 (mm) REVERT: D 347 MET cc_start: 0.8375 (tpp) cc_final: 0.7951 (tpp) REVERT: E 294 GLU cc_start: 0.7929 (tp30) cc_final: 0.7437 (tp30) REVERT: E 347 MET cc_start: 0.8205 (tpp) cc_final: 0.7665 (mpp) REVERT: F 348 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8208 (mp10) REVERT: G 347 MET cc_start: 0.8221 (mmm) cc_final: 0.7935 (mmm) REVERT: H 347 MET cc_start: 0.8366 (tpp) cc_final: 0.8065 (tpp) REVERT: H 352 GLN cc_start: 0.8975 (mp10) cc_final: 0.8630 (mp10) REVERT: I 294 GLU cc_start: 0.7875 (tp30) cc_final: 0.7517 (tp30) REVERT: J 317 THR cc_start: 0.8945 (m) cc_final: 0.8722 (p) REVERT: K 347 MET cc_start: 0.8486 (tpp) cc_final: 0.8125 (tpp) REVERT: L 317 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8893 (p) REVERT: L 324 LYS cc_start: 0.8405 (mttp) cc_final: 0.8178 (mttp) REVERT: L 347 MET cc_start: 0.8595 (tpp) cc_final: 0.8308 (tpp) REVERT: N 334 ARG cc_start: 0.7979 (ttm170) cc_final: 0.7567 (mtt90) REVERT: N 347 MET cc_start: 0.8475 (mmm) cc_final: 0.8225 (mmm) REVERT: O 294 GLU cc_start: 0.7740 (tp30) cc_final: 0.7420 (tp30) REVERT: Q 345 THR cc_start: 0.8785 (m) cc_final: 0.8480 (p) REVERT: Q 347 MET cc_start: 0.8249 (tpp) cc_final: 0.7705 (mpp) REVERT: R 294 GLU cc_start: 0.8055 (tp30) cc_final: 0.7706 (tp30) REVERT: R 339 LEU cc_start: 0.8346 (tp) cc_final: 0.8082 (tt) REVERT: R 347 MET cc_start: 0.8187 (tpp) cc_final: 0.7686 (tpp) REVERT: S 294 GLU cc_start: 0.7863 (tp30) cc_final: 0.7367 (tp30) REVERT: S 347 MET cc_start: 0.8138 (tpp) cc_final: 0.7786 (mpp) REVERT: T 345 THR cc_start: 0.8821 (t) cc_final: 0.8513 (p) REVERT: T 347 MET cc_start: 0.8367 (tpp) cc_final: 0.7840 (tpp) REVERT: X 342 SER cc_start: 0.8776 (t) cc_final: 0.8436 (p) REVERT: X 347 MET cc_start: 0.8175 (tpp) cc_final: 0.7930 (mtt) REVERT: Y 318 LEU cc_start: 0.9118 (mm) cc_final: 0.8794 (mp) REVERT: Z 294 GLU cc_start: 0.7716 (tp30) cc_final: 0.7422 (tp30) REVERT: Z 341 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8614 (m) REVERT: b 294 GLU cc_start: 0.7906 (tp30) cc_final: 0.7519 (tp30) REVERT: c 347 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8134 (mmm) REVERT: h 288 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7471 (mm) outliers start: 40 outliers final: 28 residues processed: 547 average time/residue: 0.1002 time to fit residues: 87.8134 Evaluate side-chains 557 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 524 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 342 SER Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain M residue 342 SER Chi-restraints excluded: chain N residue 342 SER Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain S residue 348 GLN Chi-restraints excluded: chain U residue 342 SER Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 324 LYS Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain V residue 342 SER Chi-restraints excluded: chain W residue 342 SER Chi-restraints excluded: chain X residue 291 LEU Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain Z residue 341 SER Chi-restraints excluded: chain Z residue 342 SER Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 342 SER Chi-restraints excluded: chain b residue 342 SER Chi-restraints excluded: chain c residue 347 MET Chi-restraints excluded: chain f residue 342 SER Chi-restraints excluded: chain h residue 288 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 81 optimal weight: 0.0060 chunk 156 optimal weight: 6.9990 chunk 179 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 177 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 94 optimal weight: 0.4980 chunk 146 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 307 GLN I 307 GLN N 307 GLN S 307 GLN U 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.167005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.147477 restraints weight = 27243.987| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 3.11 r_work: 0.3815 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18020 Z= 0.132 Angle : 0.826 15.483 24378 Z= 0.336 Chirality : 0.042 0.355 2890 Planarity : 0.005 0.052 3230 Dihedral : 4.040 24.324 2550 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.69 % Allowed : 29.30 % Favored : 69.01 % 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: 1.90 (0.18), residues: 2278 helix: 1.50 (0.12), residues: 2074 sheet: None (None), residues: 0 loop : -0.79 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 334 TYR 0.005 0.001 TYR b 284 PHE 0.022 0.003 PHE L 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (18020) covalent geometry : angle 0.82614 / 0.34 (24378) hydrogen bonds : bond 0.03252 / 2.17 ( 1293) hydrogen bonds : angle 3.80909 / 2.60 ( 3879) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 499 time to evaluate : 0.570 Fit side-chains REVERT: A 294 GLU cc_start: 0.7666 (tp30) cc_final: 0.7312 (tp30) REVERT: B 347 MET cc_start: 0.8043 (tpp) cc_final: 0.7678 (tpp) REVERT: C 288 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7441 (mm) REVERT: D 347 MET cc_start: 0.8279 (tpp) cc_final: 0.7908 (tpp) REVERT: E 294 GLU cc_start: 0.7872 (tp30) cc_final: 0.7316 (tp30) REVERT: E 347 MET cc_start: 0.8240 (tpp) cc_final: 0.7700 (mpp) REVERT: G 347 MET cc_start: 0.8269 (mmm) cc_final: 0.8025 (mmm) REVERT: H 347 MET cc_start: 0.8316 (tpp) cc_final: 0.8003 (tpp) REVERT: I 294 GLU cc_start: 0.7845 (tp30) cc_final: 0.7498 (tp30) REVERT: I 349 PHE cc_start: 0.7961 (m-80) cc_final: 0.7747 (t80) REVERT: J 317 THR cc_start: 0.9039 (m) cc_final: 0.8723 (p) REVERT: J 345 THR cc_start: 0.8670 (m) cc_final: 0.8232 (p) REVERT: K 347 MET cc_start: 0.8438 (tpp) cc_final: 0.8049 (tpp) REVERT: L 324 LYS cc_start: 0.8389 (mttp) cc_final: 0.8180 (mttp) REVERT: L 347 MET cc_start: 0.8571 (tpp) cc_final: 0.8209 (tpp) REVERT: O 294 GLU cc_start: 0.7707 (tp30) cc_final: 0.7415 (tp30) REVERT: O 349 PHE cc_start: 0.7699 (m-80) cc_final: 0.7452 (t80) REVERT: Q 345 THR cc_start: 0.8768 (m) cc_final: 0.8436 (p) REVERT: Q 347 MET cc_start: 0.8313 (tpp) cc_final: 0.7639 (mpp) REVERT: R 294 GLU cc_start: 0.7889 (tp30) cc_final: 0.7359 (tp30) REVERT: R 339 LEU cc_start: 0.8272 (tp) cc_final: 0.7996 (tt) REVERT: R 347 MET cc_start: 0.8023 (tpp) cc_final: 0.7591 (tpp) REVERT: S 294 GLU cc_start: 0.7792 (tp30) cc_final: 0.7199 (tp30) REVERT: S 347 MET cc_start: 0.8186 (tpp) cc_final: 0.7907 (mpp) REVERT: T 345 THR cc_start: 0.8764 (t) cc_final: 0.8450 (p) REVERT: T 347 MET cc_start: 0.8322 (tpp) cc_final: 0.7877 (tpp) REVERT: V 347 MET cc_start: 0.8278 (tpp) cc_final: 0.7724 (tpp) REVERT: X 342 SER cc_start: 0.8691 (t) cc_final: 0.8368 (p) REVERT: Y 334 ARG cc_start: 0.7942 (ttm170) cc_final: 0.7404 (mtt-85) REVERT: b 294 GLU cc_start: 0.7807 (tp30) cc_final: 0.7401 (tp30) REVERT: c 347 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8139 (mmm) REVERT: g 347 MET cc_start: 0.8056 (tpp) cc_final: 0.7726 (tpp) REVERT: h 288 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7497 (mm) outliers start: 31 outliers final: 23 residues processed: 506 average time/residue: 0.0940 time to fit residues: 77.0623 Evaluate side-chains 524 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 498 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain M residue 342 SER Chi-restraints excluded: chain N residue 342 SER Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain S residue 348 GLN Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain V residue 342 SER Chi-restraints excluded: chain X residue 291 LEU Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 341 SER Chi-restraints excluded: chain Z residue 341 SER Chi-restraints excluded: chain Z residue 342 SER Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 342 SER Chi-restraints excluded: chain b residue 342 SER Chi-restraints excluded: chain c residue 334 ARG Chi-restraints excluded: chain c residue 347 MET Chi-restraints excluded: chain d residue 348 GLN Chi-restraints excluded: chain f residue 342 SER Chi-restraints excluded: chain h residue 288 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 93 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 135 optimal weight: 0.0980 chunk 195 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 203 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 307 GLN S 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.167296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.148300 restraints weight = 27303.721| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.96 r_work: 0.3828 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18020 Z= 0.133 Angle : 0.819 15.291 24378 Z= 0.332 Chirality : 0.042 0.379 2890 Planarity : 0.005 0.052 3230 Dihedral : 3.950 18.240 2550 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.80 % Allowed : 29.08 % Favored : 69.12 % 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: 1.94 (0.18), residues: 2278 helix: 1.53 (0.12), residues: 2074 sheet: None (None), residues: 0 loop : -0.82 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 334 TYR 0.003 0.001 TYR e 284 PHE 0.025 0.002 PHE J 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (18020) covalent geometry : angle 0.81880 / 0.33 (24378) hydrogen bonds : bond 0.03269 / 2.19 ( 1293) hydrogen bonds : angle 3.81488 / 2.60 ( 3879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3298.01 seconds wall clock time: 57 minutes 19.27 seconds (3439.27 seconds total)