Starting phenix.real_space_refine on Wed Aug 5 01:48:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9m_49173/08_2026/9n9m_49173_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9m_49173/08_2026/9n9m_49173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n9m_49173/08_2026/9n9m_49173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9m_49173/08_2026/9n9m_49173.map" model { file = "/net/cci-nas-00/data/ceres_data/9n9m_49173/08_2026/9n9m_49173_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9m_49173/08_2026/9n9m_49173_neut.cif" } resolution = 3.38 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 100 5.49 5 S 30 5.16 5 C 4736 2.51 5 N 1428 2.21 5 O 1701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7995 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3016 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 357} Chain: "B" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2860 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 338} Chain breaks: 1 Chain: "a" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Classifications: {'DNA': 6} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 5} Chain: "b" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "c" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1692 Classifications: {'RNA': 79} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 42, 'rna3p_pyr': 31} Link IDs: {'rna2p': 6, 'rna3p': 72} Time building chain proxies: 1.88, per 1000 atoms: 0.24 Number of scatterers: 7995 At special positions: 0 Unit cell: (105.216, 102.75, 93.708, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 100 15.00 O 1701 8.00 N 1428 7.00 C 4736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 284.0 milliseconds 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1342 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 49.2% alpha, 22.2% beta 35 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 20 through 64 removed outlier: 3.834A pdb=" N GLN A 52 " --> pdb=" O HIS A 48 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 97 Processing helix chain 'A' and resid 101 through 119 removed outlier: 4.123A pdb=" N LEU A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.680A pdb=" N LEU A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 270 removed outlier: 3.685A pdb=" N TYR A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.963A pdb=" N LYS A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 283 through 291 removed outlier: 3.709A pdb=" N TYR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 315 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'B' and resid 20 through 54 Processing helix chain 'B' and resid 55 through 58 Processing helix chain 'B' and resid 84 through 97 removed outlier: 4.494A pdb=" N THR B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 248 through 272 removed outlier: 4.916A pdb=" N ARG B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 315 removed outlier: 5.874A pdb=" N ALA B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL B 286 " --> pdb=" O LYS B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 removed outlier: 3.704A pdb=" N PHE A 139 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE A 204 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A 158 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA A 157 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR A 151 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N CYS A 159 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 149 " --> pdb=" O CYS A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 71 removed outlier: 6.636A pdb=" N LYS A 68 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU A 80 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ALA A 70 " --> pdb=" O LEU A 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 246 removed outlier: 3.674A pdb=" N VAL A 236 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ALA A 317 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL A 223 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.520A pdb=" N PHE B 139 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 204 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 13 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE B 158 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA B 157 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR B 151 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N CYS B 159 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 149 " --> pdb=" O CYS B 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.520A pdb=" N PHE B 139 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 242 through 246 removed outlier: 3.688A pdb=" N THR B 239 " --> pdb=" O ASN B 242 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 244 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 237 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ALA B 317 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL B 223 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR B 319 " --> pdb=" O VAL B 223 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2025 1.34 - 1.46: 2170 1.46 - 1.58: 3916 1.58 - 1.70: 197 1.70 - 1.82: 52 Bond restraints: 8360 Sorted by residual: bond pdb=" C3' DG a 0 " pdb=" C2' DG a 0 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.78e+00 bond pdb=" C3' DC a -5 " pdb=" C2' DC a -5 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.63e+00 bond pdb=" C3' DC b 2 " pdb=" C2' DC b 2 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.50e+00 bond pdb=" C3' DT a -4 " pdb=" C2' DT a -4 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.44e+00 bond pdb=" C3' DG b 1 " pdb=" C2' DG b 1 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.09e+00 ... (remaining 8355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 11493 2.55 - 5.10: 186 5.10 - 7.65: 14 7.65 - 10.20: 1 10.20 - 12.75: 2 Bond angle restraints: 11696 Sorted by residual: angle pdb=" N VAL A 338 " pdb=" CA VAL A 338 " pdb=" C VAL A 338 " ideal model delta sigma weight residual 107.37 116.07 -8.70 1.48e+00 4.57e-01 3.46e+01 angle pdb=" C ARG A 340 " pdb=" CA ARG A 340 " pdb=" CB ARG A 340 " ideal model delta sigma weight residual 116.63 110.31 6.32 1.16e+00 7.43e-01 2.97e+01 angle pdb=" C1' C c 13 " pdb=" N1 C c 13 " pdb=" C2 C c 13 " ideal model delta sigma weight residual 118.80 123.98 -5.18 1.10e+00 8.26e-01 2.22e+01 angle pdb=" N3 DT b 3 " pdb=" C4 DT b 3 " pdb=" O4 DT b 3 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N1 C c 13 " pdb=" C2 C c 13 " pdb=" O2 C c 13 " ideal model delta sigma weight residual 118.90 121.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 11691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 4678 34.43 - 68.85: 391 68.85 - 103.28: 25 103.28 - 137.70: 1 137.70 - 172.13: 1 Dihedral angle restraints: 5096 sinusoidal: 3011 harmonic: 2085 Sorted by residual: dihedral pdb=" O4' C c 13 " pdb=" C1' C c 13 " pdb=" N1 C c 13 " pdb=" C2 C c 13 " ideal model delta sinusoidal sigma weight residual 200.00 27.87 172.13 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U c 25 " pdb=" C1' U c 25 " pdb=" N1 U c 25 " pdb=" C2 U c 25 " ideal model delta sinusoidal sigma weight residual -160.00 -54.89 -105.11 1 1.50e+01 4.44e-03 5.38e+01 dihedral pdb=" CA PHE A 337 " pdb=" C PHE A 337 " pdb=" N VAL A 338 " pdb=" CA VAL A 338 " ideal model delta harmonic sigma weight residual -180.00 -146.84 -33.16 0 5.00e+00 4.00e-02 4.40e+01 ... (remaining 5093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 832 0.036 - 0.072: 296 0.072 - 0.107: 104 0.107 - 0.143: 105 0.143 - 0.179: 7 Chirality restraints: 1344 Sorted by residual: chirality pdb=" C3' DC b -6 " pdb=" C4' DC b -6 " pdb=" O3' DC b -6 " pdb=" C2' DC b -6 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CG LEU A 69 " pdb=" CB LEU A 69 " pdb=" CD1 LEU A 69 " pdb=" CD2 LEU A 69 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE A 235 " pdb=" N ILE A 235 " pdb=" C ILE A 235 " pdb=" CB ILE A 235 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 1341 not shown) Planarity restraints: 1097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G c 28 " 0.037 2.00e-02 2.50e+03 1.58e-02 7.52e+00 pdb=" N9 G c 28 " -0.037 2.00e-02 2.50e+03 pdb=" C8 G c 28 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G c 28 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G c 28 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G c 28 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G c 28 " 0.005 2.00e-02 2.50e+03 pdb=" N1 G c 28 " 0.007 2.00e-02 2.50e+03 pdb=" C2 G c 28 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G c 28 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G c 28 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G c 28 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 326 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C GLU A 326 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU A 326 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 327 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A c 53 " 0.028 2.00e-02 2.50e+03 1.23e-02 4.13e+00 pdb=" N9 A c 53 " -0.028 2.00e-02 2.50e+03 pdb=" C8 A c 53 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A c 53 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A c 53 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A c 53 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A c 53 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A c 53 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A c 53 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A c 53 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A c 53 " -0.002 2.00e-02 2.50e+03 ... (remaining 1094 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 434 2.71 - 3.26: 7524 3.26 - 3.81: 14233 3.81 - 4.35: 17123 4.35 - 4.90: 26448 Nonbonded interactions: 65762 Sorted by model distance: nonbonded pdb=" O ARG A 84 " pdb=" OG1 THR A 87 " model vdw 2.165 3.040 nonbonded pdb=" O TYR A 272 " pdb=" NH1 ARG B 300 " model vdw 2.251 3.120 nonbonded pdb=" ND2 ASN A 324 " pdb=" CG GLU A 326 " model vdw 2.257 3.520 nonbonded pdb=" OG SER B 147 " pdb=" O ARG B 161 " model vdw 2.258 3.040 nonbonded pdb=" N MET B 1 " pdb=" OP1 U c 36 " model vdw 2.281 3.120 ... (remaining 65757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 63 or resid 83 through 365)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 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 0.042 8360 Z= 0.301 Angle : 0.762 12.750 11696 Z= 0.539 Chirality : 0.052 0.179 1344 Planarity : 0.004 0.035 1097 Dihedral : 20.738 172.130 3754 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.25 % Favored : 94.33 % Rotamer: Outliers : 3.47 % Allowed : 26.03 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.33), residues: 705 helix: 1.33 (0.28), residues: 326 sheet: -1.54 (0.47), residues: 117 loop : -1.42 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 274 TYR 0.019 0.002 TYR A 50 PHE 0.015 0.002 PHE A 39 TRP 0.021 0.001 TRP A 124 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.30 ( 8360) covalent geometry : angle 0.76175 / 0.54 (11696) hydrogen bonds : bond 0.15195 / 10.01 ( 424) hydrogen bonds : angle 6.13300 / 4.21 ( 1157) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 62 SER cc_start: 0.7538 (m) cc_final: 0.7080 (m) REVERT: A 97 LYS cc_start: 0.7779 (ttpp) cc_final: 0.7544 (ttmt) REVERT: A 211 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6821 (mm-30) REVERT: A 229 LEU cc_start: 0.3600 (OUTLIER) cc_final: 0.2532 (mp) REVERT: A 308 LEU cc_start: 0.7787 (tp) cc_final: 0.7451 (tp) REVERT: A 357 LYS cc_start: 0.8625 (tttt) cc_final: 0.8401 (ttpp) REVERT: B 28 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.5357 (tpp) REVERT: B 85 MET cc_start: 0.2443 (mmt) cc_final: 0.2208 (mmt) REVERT: B 170 TYR cc_start: 0.6468 (t80) cc_final: 0.6101 (t80) REVERT: B 220 LYS cc_start: 0.7705 (mttt) cc_final: 0.7262 (mttt) REVERT: B 307 LYS cc_start: 0.6525 (tppt) cc_final: 0.6164 (tppt) outliers start: 22 outliers final: 6 residues processed: 175 average time/residue: 0.1145 time to fit residues: 25.5145 Evaluate side-chains 151 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 108 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.201425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.165425 restraints weight = 12172.297| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.56 r_work: 0.3769 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.154 8360 Z= 0.570 Angle : 1.130 15.450 11696 Z= 0.607 Chirality : 0.070 0.307 1344 Planarity : 0.011 0.150 1097 Dihedral : 21.119 165.385 2238 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.96 % Favored : 93.48 % Rotamer: Outliers : 7.57 % Allowed : 25.08 % Favored : 67.35 % 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: -1.35 (0.30), residues: 705 helix: -0.10 (0.26), residues: 322 sheet: -1.35 (0.50), residues: 103 loop : -1.54 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 265 TYR 0.040 0.005 TYR B 123 PHE 0.043 0.005 PHE A 139 TRP 0.020 0.004 TRP A 124 HIS 0.011 0.003 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.01193 / 0.57 ( 8360) covalent geometry : angle 1.12986 / 0.61 (11696) hydrogen bonds : bond 0.08849 / 6.11 ( 424) hydrogen bonds : angle 5.65338 / 3.99 ( 1157) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 9 THR cc_start: 0.7958 (m) cc_final: 0.7577 (p) REVERT: A 46 VAL cc_start: 0.7373 (OUTLIER) cc_final: 0.6852 (m) REVERT: A 62 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.8004 (m) REVERT: A 124 TRP cc_start: 0.5111 (OUTLIER) cc_final: 0.3947 (m-10) REVERT: A 127 GLU cc_start: 0.7352 (mp0) cc_final: 0.7095 (mp0) REVERT: A 160 PHE cc_start: 0.8281 (p90) cc_final: 0.7535 (p90) REVERT: A 211 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7182 (mm-30) REVERT: A 229 LEU cc_start: 0.5094 (OUTLIER) cc_final: 0.4751 (mp) REVERT: A 312 CYS cc_start: 0.7448 (m) cc_final: 0.6994 (t) REVERT: A 315 HIS cc_start: 0.7767 (m90) cc_final: 0.7552 (m90) REVERT: B 28 MET cc_start: 0.5883 (tpp) cc_final: 0.5437 (tpp) REVERT: B 53 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: B 58 PHE cc_start: 0.7439 (m-80) cc_final: 0.6710 (t80) REVERT: B 85 MET cc_start: 0.2380 (mmt) cc_final: 0.2160 (mmt) REVERT: B 118 LYS cc_start: 0.7808 (mttt) cc_final: 0.7482 (mttt) REVERT: B 170 TYR cc_start: 0.7164 (t80) cc_final: 0.6942 (t80) REVERT: B 178 LYS cc_start: 0.7977 (mttt) cc_final: 0.7752 (mttt) REVERT: B 197 ILE cc_start: 0.7582 (mm) cc_final: 0.7360 (mm) REVERT: B 220 LYS cc_start: 0.7792 (mttt) cc_final: 0.7350 (mttt) REVERT: B 245 THR cc_start: 0.8443 (m) cc_final: 0.8084 (t) REVERT: B 246 ILE cc_start: 0.8065 (mm) cc_final: 0.7795 (mt) REVERT: B 307 LYS cc_start: 0.6842 (tppt) cc_final: 0.6607 (tppt) outliers start: 48 outliers final: 23 residues processed: 182 average time/residue: 0.1180 time to fit residues: 27.3583 Evaluate side-chains 171 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 342 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.206439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.171116 restraints weight = 12186.336| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.49 r_work: 0.3853 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8360 Z= 0.170 Angle : 0.644 8.622 11696 Z= 0.365 Chirality : 0.043 0.200 1344 Planarity : 0.005 0.062 1097 Dihedral : 20.955 165.619 2233 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.96 % Favored : 94.61 % Rotamer: Outliers : 5.21 % Allowed : 26.50 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.32), residues: 705 helix: 1.03 (0.28), residues: 327 sheet: -1.71 (0.46), residues: 113 loop : -1.41 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 128 TYR 0.025 0.002 TYR B 123 PHE 0.022 0.002 PHE B 252 TRP 0.014 0.002 TRP B 342 HIS 0.007 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 8360) covalent geometry : angle 0.64434 / 0.36 (11696) hydrogen bonds : bond 0.05863 / 4.01 ( 424) hydrogen bonds : angle 4.73902 / 3.32 ( 1157) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7295 (tpp) cc_final: 0.7074 (tpp) REVERT: A 53 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: A 61 LEU cc_start: 0.8359 (tt) cc_final: 0.8064 (tt) REVERT: A 106 SER cc_start: 0.7124 (t) cc_final: 0.6825 (m) REVERT: A 123 TYR cc_start: 0.7186 (m-80) cc_final: 0.6877 (m-80) REVERT: A 124 TRP cc_start: 0.5182 (OUTLIER) cc_final: 0.4283 (m-10) REVERT: A 265 ARG cc_start: 0.6843 (ttp-170) cc_final: 0.6537 (ttp-170) REVERT: A 345 TYR cc_start: 0.4320 (OUTLIER) cc_final: 0.3614 (m-80) REVERT: A 352 LYS cc_start: 0.7530 (mmtp) cc_final: 0.7257 (mmmt) REVERT: B 28 MET cc_start: 0.5895 (tpp) cc_final: 0.5588 (tpp) REVERT: B 53 GLU cc_start: 0.7841 (tp30) cc_final: 0.7545 (tp30) REVERT: B 58 PHE cc_start: 0.7383 (m-80) cc_final: 0.6702 (t80) REVERT: B 85 MET cc_start: 0.2241 (mmt) cc_final: 0.2038 (mmt) REVERT: B 118 LYS cc_start: 0.7727 (mttt) cc_final: 0.7385 (mttt) REVERT: B 134 LYS cc_start: 0.7475 (mtpp) cc_final: 0.7240 (mtpp) REVERT: B 170 TYR cc_start: 0.7099 (t80) cc_final: 0.6842 (t80) REVERT: B 178 LYS cc_start: 0.7909 (mttt) cc_final: 0.7629 (mttt) REVERT: B 220 LYS cc_start: 0.7748 (mttt) cc_final: 0.7451 (mttt) REVERT: B 233 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.6501 (m-10) REVERT: B 246 ILE cc_start: 0.7972 (mm) cc_final: 0.7720 (mt) REVERT: B 307 LYS cc_start: 0.6873 (tppt) cc_final: 0.6633 (tppt) outliers start: 33 outliers final: 19 residues processed: 165 average time/residue: 0.1119 time to fit residues: 23.6119 Evaluate side-chains 161 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 301 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.203170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.167280 restraints weight = 12436.870| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.51 r_work: 0.3851 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8360 Z= 0.146 Angle : 0.586 7.132 11696 Z= 0.331 Chirality : 0.041 0.208 1344 Planarity : 0.005 0.062 1097 Dihedral : 20.824 165.316 2227 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.82 % Favored : 94.04 % Rotamer: Outliers : 5.21 % Allowed : 28.08 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.33), residues: 705 helix: 1.44 (0.28), residues: 333 sheet: -1.72 (0.47), residues: 113 loop : -1.43 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 35 TYR 0.019 0.002 TYR B 123 PHE 0.016 0.002 PHE A 96 TRP 0.011 0.002 TRP B 342 HIS 0.005 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 ( 8360) covalent geometry : angle 0.58569 / 0.33 (11696) hydrogen bonds : bond 0.05053 / 3.40 ( 424) hydrogen bonds : angle 4.45784 / 3.11 ( 1157) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: A 61 LEU cc_start: 0.8366 (tt) cc_final: 0.8007 (tt) REVERT: A 106 SER cc_start: 0.7151 (t) cc_final: 0.6899 (m) REVERT: A 123 TYR cc_start: 0.7143 (m-80) cc_final: 0.6791 (m-80) REVERT: A 124 TRP cc_start: 0.5326 (OUTLIER) cc_final: 0.4321 (m-10) REVERT: A 187 LYS cc_start: 0.7991 (ttpp) cc_final: 0.7507 (ttpp) REVERT: A 189 ASP cc_start: 0.6798 (m-30) cc_final: 0.6091 (m-30) REVERT: A 211 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7018 (mm-30) REVERT: A 229 LEU cc_start: 0.3730 (OUTLIER) cc_final: 0.2732 (mt) REVERT: A 265 ARG cc_start: 0.6891 (ttp-170) cc_final: 0.6539 (ttp-170) REVERT: A 345 TYR cc_start: 0.4183 (OUTLIER) cc_final: 0.3379 (m-80) REVERT: B 28 MET cc_start: 0.5930 (tpp) cc_final: 0.5722 (tpp) REVERT: B 58 PHE cc_start: 0.7278 (m-80) cc_final: 0.6685 (t80) REVERT: B 85 MET cc_start: 0.2477 (mmt) cc_final: 0.2232 (mmt) REVERT: B 118 LYS cc_start: 0.7702 (mttt) cc_final: 0.7359 (mttt) REVERT: B 124 TRP cc_start: 0.6136 (OUTLIER) cc_final: 0.5797 (m100) REVERT: B 160 PHE cc_start: 0.6260 (p90) cc_final: 0.5700 (p90) REVERT: B 170 TYR cc_start: 0.7172 (t80) cc_final: 0.6902 (t80) REVERT: B 178 LYS cc_start: 0.7911 (mttt) cc_final: 0.7648 (mttt) REVERT: B 199 LEU cc_start: 0.8043 (mp) cc_final: 0.7838 (mp) REVERT: B 220 LYS cc_start: 0.7780 (mttt) cc_final: 0.7494 (mttt) REVERT: B 246 ILE cc_start: 0.7996 (mm) cc_final: 0.7735 (mt) REVERT: B 307 LYS cc_start: 0.6944 (tppt) cc_final: 0.6688 (tppt) outliers start: 33 outliers final: 20 residues processed: 158 average time/residue: 0.1227 time to fit residues: 24.6270 Evaluate side-chains 162 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.0060 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 37 optimal weight: 0.3980 chunk 65 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.204963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.169214 restraints weight = 12391.621| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.51 r_work: 0.3870 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8360 Z= 0.130 Angle : 0.565 7.744 11696 Z= 0.316 Chirality : 0.040 0.197 1344 Planarity : 0.004 0.064 1097 Dihedral : 20.799 163.937 2227 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.39 % Favored : 94.47 % Rotamer: Outliers : 5.52 % Allowed : 27.13 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.33), residues: 705 helix: 1.69 (0.28), residues: 331 sheet: -1.46 (0.48), residues: 111 loop : -1.48 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 128 TYR 0.025 0.002 TYR B 344 PHE 0.014 0.002 PHE A 58 TRP 0.017 0.002 TRP A 342 HIS 0.005 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 8360) covalent geometry : angle 0.56544 / 0.32 (11696) hydrogen bonds : bond 0.04737 / 3.18 ( 424) hydrogen bonds : angle 4.31878 / 3.02 ( 1157) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: A 61 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8104 (tt) REVERT: A 106 SER cc_start: 0.7033 (t) cc_final: 0.6763 (m) REVERT: A 124 TRP cc_start: 0.5304 (OUTLIER) cc_final: 0.4287 (m-10) REVERT: A 187 LYS cc_start: 0.7891 (ttpp) cc_final: 0.7352 (ttpp) REVERT: A 189 ASP cc_start: 0.6752 (m-30) cc_final: 0.5936 (m-30) REVERT: A 211 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6980 (mm-30) REVERT: A 229 LEU cc_start: 0.3622 (OUTLIER) cc_final: 0.2649 (mt) REVERT: A 265 ARG cc_start: 0.6927 (ttp-170) cc_final: 0.6567 (ttp-170) REVERT: A 345 TYR cc_start: 0.3981 (OUTLIER) cc_final: 0.3299 (m-80) REVERT: A 352 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7383 (mmtp) REVERT: B 28 MET cc_start: 0.6071 (tpp) cc_final: 0.5772 (tpp) REVERT: B 58 PHE cc_start: 0.7223 (m-80) cc_final: 0.6748 (t80) REVERT: B 85 MET cc_start: 0.2673 (mmt) cc_final: 0.2408 (mmt) REVERT: B 105 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7334 (mp) REVERT: B 118 LYS cc_start: 0.7702 (mttt) cc_final: 0.7347 (mttt) REVERT: B 160 PHE cc_start: 0.6216 (p90) cc_final: 0.5674 (p90) REVERT: B 170 TYR cc_start: 0.7188 (t80) cc_final: 0.6910 (t80) REVERT: B 178 LYS cc_start: 0.7894 (mttt) cc_final: 0.7654 (mttt) REVERT: B 220 LYS cc_start: 0.7792 (mttt) cc_final: 0.7506 (mttt) REVERT: B 307 LYS cc_start: 0.7032 (tppt) cc_final: 0.6745 (tppt) REVERT: B 308 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5887 (mt) outliers start: 35 outliers final: 18 residues processed: 158 average time/residue: 0.1090 time to fit residues: 22.0600 Evaluate side-chains 163 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.200104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.165793 restraints weight = 12281.023| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.49 r_work: 0.3756 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8360 Z= 0.266 Angle : 0.709 13.549 11696 Z= 0.384 Chirality : 0.049 0.377 1344 Planarity : 0.005 0.069 1097 Dihedral : 20.772 164.600 2227 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.10 % Favored : 93.76 % Rotamer: Outliers : 4.73 % Allowed : 28.39 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.32), residues: 705 helix: 1.31 (0.28), residues: 326 sheet: -1.52 (0.47), residues: 111 loop : -1.41 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 128 TYR 0.020 0.003 TYR B 289 PHE 0.025 0.003 PHE A 39 TRP 0.020 0.003 TRP A 124 HIS 0.007 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.27 ( 8360) covalent geometry : angle 0.70865 / 0.38 (11696) hydrogen bonds : bond 0.05582 / 3.81 ( 424) hydrogen bonds : angle 4.60795 / 3.24 ( 1157) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 61 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8089 (tt) REVERT: A 106 SER cc_start: 0.7271 (t) cc_final: 0.7006 (m) REVERT: A 124 TRP cc_start: 0.5759 (OUTLIER) cc_final: 0.4712 (m-10) REVERT: A 211 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6952 (mm-30) REVERT: A 265 ARG cc_start: 0.7017 (ttp-170) cc_final: 0.6693 (ttp-170) REVERT: A 279 LYS cc_start: 0.7441 (mtpp) cc_final: 0.7147 (mtpp) REVERT: B 28 MET cc_start: 0.6177 (tpp) cc_final: 0.5840 (tpp) REVERT: B 85 MET cc_start: 0.2522 (mmt) cc_final: 0.2315 (mmt) REVERT: B 118 LYS cc_start: 0.7750 (mttt) cc_final: 0.7426 (mttt) REVERT: B 125 LYS cc_start: 0.7248 (mttt) cc_final: 0.7027 (tttt) REVERT: B 160 PHE cc_start: 0.6296 (p90) cc_final: 0.5733 (p90) REVERT: B 170 TYR cc_start: 0.7231 (t80) cc_final: 0.6974 (t80) REVERT: B 178 LYS cc_start: 0.7983 (mttt) cc_final: 0.7754 (mttt) REVERT: B 220 LYS cc_start: 0.7835 (mttt) cc_final: 0.7610 (mttt) REVERT: B 308 LEU cc_start: 0.6583 (tp) cc_final: 0.6195 (mt) outliers start: 30 outliers final: 23 residues processed: 159 average time/residue: 0.1032 time to fit residues: 21.2508 Evaluate side-chains 168 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 301 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.202754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.167277 restraints weight = 12249.228| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.47 r_work: 0.3805 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8360 Z= 0.172 Angle : 0.626 11.061 11696 Z= 0.344 Chirality : 0.044 0.441 1344 Planarity : 0.005 0.068 1097 Dihedral : 20.755 163.983 2225 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.82 % Favored : 94.04 % Rotamer: Outliers : 4.89 % Allowed : 28.08 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.32), residues: 705 helix: 1.40 (0.27), residues: 332 sheet: -1.58 (0.46), residues: 111 loop : -1.38 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 256 TYR 0.022 0.002 TYR A 123 PHE 0.018 0.002 PHE A 39 TRP 0.014 0.002 TRP A 342 HIS 0.005 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 8360) covalent geometry : angle 0.62562 / 0.34 (11696) hydrogen bonds : bond 0.05015 / 3.40 ( 424) hydrogen bonds : angle 4.40118 / 3.09 ( 1157) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 16 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.7169 (mt) REVERT: A 53 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7807 (mt-10) REVERT: A 61 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8074 (tt) REVERT: A 106 SER cc_start: 0.7106 (t) cc_final: 0.6885 (m) REVERT: A 187 LYS cc_start: 0.7895 (ttpp) cc_final: 0.7686 (ptmm) REVERT: A 211 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6946 (mm-30) REVERT: A 229 LEU cc_start: 0.3823 (OUTLIER) cc_final: 0.2716 (mt) REVERT: A 265 ARG cc_start: 0.6986 (ttp-170) cc_final: 0.6703 (ttp-170) REVERT: A 279 LYS cc_start: 0.7476 (mtpp) cc_final: 0.7162 (mtpp) REVERT: A 345 TYR cc_start: 0.3967 (OUTLIER) cc_final: 0.1851 (m-80) REVERT: B 28 MET cc_start: 0.6241 (tpp) cc_final: 0.5879 (tpp) REVERT: B 53 GLU cc_start: 0.7719 (tp30) cc_final: 0.7280 (tm-30) REVERT: B 58 PHE cc_start: 0.7566 (m-80) cc_final: 0.6630 (t80) REVERT: B 85 MET cc_start: 0.2804 (OUTLIER) cc_final: 0.2517 (mmt) REVERT: B 105 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7342 (mp) REVERT: B 116 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7298 (t80) REVERT: B 118 LYS cc_start: 0.7749 (mttt) cc_final: 0.7403 (mttt) REVERT: B 125 LYS cc_start: 0.7200 (mttt) cc_final: 0.6977 (tttt) REVERT: B 160 PHE cc_start: 0.6268 (p90) cc_final: 0.5676 (p90) REVERT: B 170 TYR cc_start: 0.7244 (t80) cc_final: 0.6974 (t80) REVERT: B 178 LYS cc_start: 0.7982 (mttt) cc_final: 0.7774 (mttt) REVERT: B 220 LYS cc_start: 0.7783 (mttt) cc_final: 0.7552 (mttt) REVERT: B 308 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.6049 (mt) outliers start: 31 outliers final: 18 residues processed: 158 average time/residue: 0.1179 time to fit residues: 23.8694 Evaluate side-chains 167 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 15 optimal weight: 0.0270 chunk 56 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.201149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.165645 restraints weight = 12224.099| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.46 r_work: 0.3783 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8360 Z= 0.207 Angle : 0.654 11.380 11696 Z= 0.359 Chirality : 0.045 0.372 1344 Planarity : 0.005 0.066 1097 Dihedral : 20.712 164.147 2225 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.82 % Favored : 94.04 % Rotamer: Outliers : 4.57 % Allowed : 29.02 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.32), residues: 705 helix: 1.38 (0.28), residues: 326 sheet: -1.48 (0.45), residues: 109 loop : -1.40 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 128 TYR 0.024 0.002 TYR A 123 PHE 0.020 0.002 PHE A 39 TRP 0.016 0.002 TRP A 124 HIS 0.006 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 ( 8360) covalent geometry : angle 0.65408 / 0.36 (11696) hydrogen bonds : bond 0.05106 / 3.46 ( 424) hydrogen bonds : angle 4.55167 / 3.22 ( 1157) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7835 (mt-10) REVERT: A 61 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8155 (tt) REVERT: A 211 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7059 (mm-30) REVERT: A 229 LEU cc_start: 0.3997 (OUTLIER) cc_final: 0.2980 (mt) REVERT: A 265 ARG cc_start: 0.6986 (ttp-170) cc_final: 0.6672 (ttp-170) REVERT: A 311 PHE cc_start: 0.7601 (t80) cc_final: 0.7179 (t80) REVERT: A 345 TYR cc_start: 0.3943 (OUTLIER) cc_final: 0.1775 (m-80) REVERT: B 10 ARG cc_start: 0.7183 (mmt-90) cc_final: 0.6194 (mmt-90) REVERT: B 28 MET cc_start: 0.6330 (tpp) cc_final: 0.5934 (tpp) REVERT: B 53 GLU cc_start: 0.7767 (tp30) cc_final: 0.7283 (tm-30) REVERT: B 58 PHE cc_start: 0.7556 (m-80) cc_final: 0.6658 (t80) REVERT: B 85 MET cc_start: 0.2877 (OUTLIER) cc_final: 0.2583 (mmt) REVERT: B 118 LYS cc_start: 0.7760 (mttt) cc_final: 0.7435 (mttt) REVERT: B 125 LYS cc_start: 0.7257 (mttt) cc_final: 0.7035 (tttt) REVERT: B 160 PHE cc_start: 0.6343 (p90) cc_final: 0.5778 (p90) REVERT: B 170 TYR cc_start: 0.7239 (t80) cc_final: 0.6972 (t80) REVERT: B 220 LYS cc_start: 0.7795 (mttt) cc_final: 0.7573 (mttt) REVERT: B 308 LEU cc_start: 0.6393 (tp) cc_final: 0.6048 (mp) outliers start: 29 outliers final: 23 residues processed: 164 average time/residue: 0.1067 time to fit residues: 22.6490 Evaluate side-chains 174 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 342 TRP Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 301 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 47 optimal weight: 0.0970 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.190500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.155255 restraints weight = 12292.941| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.37 r_work: 0.3751 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8360 Z= 0.271 Angle : 0.733 13.250 11696 Z= 0.400 Chirality : 0.049 0.356 1344 Planarity : 0.005 0.066 1097 Dihedral : 20.757 164.358 2225 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.10 % Favored : 93.76 % Rotamer: Outliers : 5.05 % Allowed : 29.34 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.31), residues: 705 helix: 1.06 (0.28), residues: 326 sheet: -1.56 (0.44), residues: 109 loop : -1.68 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 256 TYR 0.025 0.002 TYR A 123 PHE 0.029 0.003 PHE A 39 TRP 0.027 0.003 TRP A 124 HIS 0.008 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.27 ( 8360) covalent geometry : angle 0.73310 / 0.40 (11696) hydrogen bonds : bond 0.05741 / 3.86 ( 424) hydrogen bonds : angle 4.70250 / 3.32 ( 1157) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.6713 (m-70) REVERT: A 53 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7856 (mt-10) REVERT: A 61 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8228 (tt) REVERT: A 229 LEU cc_start: 0.4252 (OUTLIER) cc_final: 0.3148 (mt) REVERT: A 265 ARG cc_start: 0.7004 (ttp-170) cc_final: 0.6676 (ttp-170) REVERT: A 311 PHE cc_start: 0.7634 (t80) cc_final: 0.7256 (t80) REVERT: A 345 TYR cc_start: 0.3932 (OUTLIER) cc_final: 0.1956 (m-80) REVERT: B 10 ARG cc_start: 0.7131 (mmt-90) cc_final: 0.6170 (mmt-90) REVERT: B 28 MET cc_start: 0.6321 (tpp) cc_final: 0.5953 (tpp) REVERT: B 53 GLU cc_start: 0.7813 (tp30) cc_final: 0.7360 (tm-30) REVERT: B 58 PHE cc_start: 0.7478 (m-80) cc_final: 0.6798 (t80) REVERT: B 85 MET cc_start: 0.2851 (OUTLIER) cc_final: 0.2582 (mmt) REVERT: B 118 LYS cc_start: 0.7893 (mttt) cc_final: 0.7578 (mttt) REVERT: B 125 LYS cc_start: 0.7376 (mttt) cc_final: 0.7133 (tttt) REVERT: B 170 TYR cc_start: 0.7265 (t80) cc_final: 0.7008 (t80) REVERT: B 220 LYS cc_start: 0.7825 (mttt) cc_final: 0.7591 (mttt) REVERT: B 308 LEU cc_start: 0.6661 (tp) cc_final: 0.6442 (mt) outliers start: 32 outliers final: 20 residues processed: 161 average time/residue: 0.1078 time to fit residues: 22.1563 Evaluate side-chains 169 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 342 TRP Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 301 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 9.9990 chunk 61 optimal weight: 50.0000 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.202098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.166273 restraints weight = 12214.998| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.49 r_work: 0.3797 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8360 Z= 0.143 Angle : 0.616 10.790 11696 Z= 0.341 Chirality : 0.042 0.249 1344 Planarity : 0.004 0.061 1097 Dihedral : 20.749 162.527 2225 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.38 % Favored : 93.48 % Rotamer: Outliers : 3.94 % Allowed : 30.76 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.32), residues: 705 helix: 1.44 (0.28), residues: 330 sheet: -1.34 (0.45), residues: 101 loop : -1.64 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 256 TYR 0.021 0.002 TYR A 60 PHE 0.018 0.002 PHE A 96 TRP 0.032 0.002 TRP B 124 HIS 0.004 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 8360) covalent geometry : angle 0.61561 / 0.34 (11696) hydrogen bonds : bond 0.04851 / 3.24 ( 424) hydrogen bonds : angle 4.43643 / 3.15 ( 1157) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: A 61 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8243 (tp) REVERT: A 211 GLU cc_start: 0.7255 (mt-10) cc_final: 0.7015 (mm-30) REVERT: A 265 ARG cc_start: 0.7031 (ttp-170) cc_final: 0.6765 (ttp-170) REVERT: A 342 TRP cc_start: 0.3465 (OUTLIER) cc_final: 0.2821 (m100) REVERT: A 345 TYR cc_start: 0.3832 (OUTLIER) cc_final: 0.2062 (m-80) REVERT: B 10 ARG cc_start: 0.7150 (mmt-90) cc_final: 0.6238 (mmt-90) REVERT: B 28 MET cc_start: 0.6339 (tpp) cc_final: 0.5949 (tpp) REVERT: B 52 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: B 53 GLU cc_start: 0.7749 (tp30) cc_final: 0.7251 (tm-30) REVERT: B 58 PHE cc_start: 0.7479 (m-80) cc_final: 0.6730 (t80) REVERT: B 85 MET cc_start: 0.3013 (OUTLIER) cc_final: 0.2686 (mmt) REVERT: B 118 LYS cc_start: 0.7841 (mttt) cc_final: 0.7523 (mttt) REVERT: B 125 LYS cc_start: 0.7321 (mttt) cc_final: 0.7066 (tttt) REVERT: B 153 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 170 TYR cc_start: 0.7236 (t80) cc_final: 0.6936 (t80) REVERT: B 220 LYS cc_start: 0.7790 (mttt) cc_final: 0.7531 (mttt) outliers start: 25 outliers final: 15 residues processed: 156 average time/residue: 0.1165 time to fit residues: 23.1983 Evaluate side-chains 160 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 342 TRP Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.188420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.153052 restraints weight = 12350.522| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.42 r_work: 0.3716 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 8360 Z= 0.347 Angle : 0.810 12.802 11696 Z= 0.436 Chirality : 0.055 0.533 1344 Planarity : 0.006 0.063 1097 Dihedral : 20.741 164.620 2225 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.38 % Favored : 93.48 % Rotamer: Outliers : 4.10 % Allowed : 30.76 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.31), residues: 705 helix: 0.85 (0.27), residues: 324 sheet: -1.45 (0.44), residues: 107 loop : -1.73 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 281 TYR 0.017 0.003 TYR B 233 PHE 0.033 0.003 PHE A 39 TRP 0.031 0.004 TRP A 124 HIS 0.008 0.002 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.35 ( 8360) covalent geometry : angle 0.80988 / 0.44 (11696) hydrogen bonds : bond 0.06115 / 4.09 ( 424) hydrogen bonds : angle 4.81897 / 3.41 ( 1157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1813.15 seconds wall clock time: 31 minutes 49.67 seconds (1909.67 seconds total)