Starting phenix.real_space_refine on Thu Jul 2 09:19:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9m_49173/07_2026/9n9m_49173_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9m_49173/07_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_49173/07_2026/9n9m_49173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9m_49173/07_2026/9n9m_49173.map" model { file = "/net/cci-nas-00/data/ceres_data/9n9m_49173/07_2026/9n9m_49173_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9m_49173/07_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-dev-6108/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: 2.06, per 1000 atoms: 0.26 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: 0.79 Conformation dependent library (CDL) restraints added in 351.1 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: 0.98 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: 1.38 Time building geometry restraints manager: 1.00 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: 11577 2.55 - 5.10: 102 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: 918 0.036 - 0.072: 289 0.072 - 0.107: 101 0.107 - 0.143: 31 0.143 - 0.179: 5 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: 1.270 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.750 Find NCS groups from input model: 0.100 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.550 ------------------------------------------------------------------------------- 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= 0.292 Angle : 0.685 12.750 11696 Z= 0.469 Chirality : 0.042 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 0.00402 / 0.29 ( 8360) covalent geometry : angle 0.68458 / 0.47 (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 : 0.283 Fit side-chains revert: symmetry clash REVERT: A 62 SER cc_start: 0.7538 (m) cc_final: 0.7081 (m) REVERT: A 97 LYS cc_start: 0.7779 (ttpp) cc_final: 0.7528 (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: 0.2533 (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: 0.2211 (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: 0.6163 (tppt) outliers start: 22 outliers final: 6 residues processed: 175 average time/residue: 0.1163 time to fit residues: 25.8285 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 : 0.240 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.4403 r_free = 0.4403 target = 0.201724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.165712 restraints weight = 12172.326| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.60 r_work: 0.3774 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.157 8360 Z= 0.557 Angle : 1.096 15.226 11696 Z= 0.600 Chirality : 0.068 0.313 1344 Planarity : 0.010 0.126 1097 Dihedral : 21.290 164.086 2238 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.38 % Favored : 93.19 % Rotamer: Outliers : 8.04 % Allowed : 25.24 % Favored : 66.72 % 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: -1.42 (0.30), residues: 705 helix: -0.14 (0.26), residues: 316 sheet: -1.34 (0.50), residues: 103 loop : -1.60 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B 184 TYR 0.034 0.005 TYR B 123 PHE 0.045 0.005 PHE B 252 TRP 0.019 0.004 TRP A 124 HIS 0.010 0.003 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.01164 / 0.56 ( 8360) covalent geometry : angle 1.09618 / 0.60 (11696) hydrogen bonds : bond 0.09058 / 6.25 ( 424) hydrogen bonds : angle 5.71694 / 4.04 ( 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: 51 poor density : 149 time to evaluate : 0.217 Fit side-chains REVERT: A 9 THR cc_start: 0.7951 (m) cc_final: 0.7571 (p) REVERT: A 46 VAL cc_start: 0.7351 (OUTLIER) cc_final: 0.6818 (m) REVERT: A 62 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.8050 (m) REVERT: A 106 SER cc_start: 0.7415 (t) cc_final: 0.6978 (m) REVERT: A 124 TRP cc_start: 0.5133 (OUTLIER) cc_final: 0.3905 (m-10) REVERT: A 127 GLU cc_start: 0.7373 (mp0) cc_final: 0.7020 (mp0) REVERT: A 160 PHE cc_start: 0.8275 (p90) cc_final: 0.7527 (p90) REVERT: A 229 LEU cc_start: 0.5119 (OUTLIER) cc_final: 0.4779 (mp) REVERT: A 312 CYS cc_start: 0.7412 (m) cc_final: 0.6960 (t) REVERT: A 315 HIS cc_start: 0.7797 (m90) cc_final: 0.7583 (m90) REVERT: A 357 LYS cc_start: 0.8667 (tttt) cc_final: 0.8449 (ttpp) REVERT: B 28 MET cc_start: 0.5888 (tpp) cc_final: 0.5446 (tpp) REVERT: B 53 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: B 58 PHE cc_start: 0.7415 (m-80) cc_final: 0.6705 (t80) REVERT: B 85 MET cc_start: 0.2376 (mmt) cc_final: 0.2158 (mmt) REVERT: B 118 LYS cc_start: 0.7807 (mttt) cc_final: 0.7480 (mttt) REVERT: B 170 TYR cc_start: 0.7175 (t80) cc_final: 0.6953 (t80) REVERT: B 197 ILE cc_start: 0.7590 (mm) cc_final: 0.7364 (mm) REVERT: B 220 LYS cc_start: 0.7780 (mttt) cc_final: 0.7346 (mttt) REVERT: B 245 THR cc_start: 0.8438 (m) cc_final: 0.8078 (t) REVERT: B 246 ILE cc_start: 0.8053 (mm) cc_final: 0.7793 (mt) REVERT: B 307 LYS cc_start: 0.6846 (tppt) cc_final: 0.6606 (tppt) REVERT: B 351 ILE cc_start: 0.7589 (tt) cc_final: 0.7341 (pt) outliers start: 51 outliers final: 23 residues processed: 180 average time/residue: 0.1184 time to fit residues: 27.1038 Evaluate side-chains 170 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 60 TYR 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 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: 0.9990 chunk 38 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 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** ** B 242 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 = 0.4440 r_free = 0.4440 target = 0.202822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.167123 restraints weight = 12155.696| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.49 r_work: 0.3842 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8360 Z= 0.178 Angle : 0.653 9.050 11696 Z= 0.370 Chirality : 0.044 0.204 1344 Planarity : 0.005 0.056 1097 Dihedral : 21.051 164.389 2233 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.96 % Favored : 94.61 % Rotamer: Outliers : 5.21 % Allowed : 26.97 % Favored : 67.82 % 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: -0.61 (0.32), residues: 705 helix: 0.88 (0.28), residues: 327 sheet: -1.65 (0.48), residues: 113 loop : -1.38 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 120 TYR 0.023 0.002 TYR B 123 PHE 0.022 0.002 PHE B 252 TRP 0.010 0.002 TRP A 342 HIS 0.004 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 ( 8360) covalent geometry : angle 0.65326 / 0.37 (11696) hydrogen bonds : bond 0.05995 / 4.10 ( 424) hydrogen bonds : angle 4.83051 / 3.39 ( 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 180 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 THR cc_start: 0.7860 (m) cc_final: 0.7459 (p) REVERT: A 30 MET cc_start: 0.7284 (tpp) cc_final: 0.7084 (tpp) REVERT: A 53 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: A 61 LEU cc_start: 0.8280 (tt) cc_final: 0.8009 (tt) REVERT: A 62 SER cc_start: 0.8282 (m) cc_final: 0.7992 (m) REVERT: A 106 SER cc_start: 0.7095 (t) cc_final: 0.6769 (m) REVERT: A 123 TYR cc_start: 0.7256 (m-80) cc_final: 0.6923 (m-80) REVERT: A 124 TRP cc_start: 0.5183 (OUTLIER) cc_final: 0.4247 (m-10) REVERT: A 160 PHE cc_start: 0.8209 (p90) cc_final: 0.7487 (p90) REVERT: A 189 ASP cc_start: 0.6971 (m-30) cc_final: 0.6757 (m-30) REVERT: A 265 ARG cc_start: 0.6947 (ttp-170) cc_final: 0.6709 (ttp-170) REVERT: A 352 LYS cc_start: 0.7555 (mmtp) cc_final: 0.7331 (mmmt) REVERT: B 28 MET cc_start: 0.5905 (tpp) cc_final: 0.5573 (tpp) REVERT: B 53 GLU cc_start: 0.7862 (tp30) cc_final: 0.7558 (tp30) REVERT: B 58 PHE cc_start: 0.7369 (m-80) cc_final: 0.6696 (t80) REVERT: B 85 MET cc_start: 0.2221 (mmt) cc_final: 0.2015 (mmt) REVERT: B 118 LYS cc_start: 0.7720 (mttt) cc_final: 0.7368 (mttt) REVERT: B 134 LYS cc_start: 0.7449 (mtpp) cc_final: 0.7216 (mtpp) REVERT: B 170 TYR cc_start: 0.7107 (t80) cc_final: 0.6867 (t80) REVERT: B 220 LYS cc_start: 0.7778 (mttt) cc_final: 0.7484 (mttt) REVERT: B 307 LYS cc_start: 0.6862 (tppt) cc_final: 0.6641 (tppt) REVERT: B 308 LEU cc_start: 0.6330 (tp) cc_final: 0.5325 (mt) outliers start: 33 outliers final: 21 residues processed: 166 average time/residue: 0.1143 time to fit residues: 24.4220 Evaluate side-chains 168 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 115 SER Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 280 LYS 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 249 LYS Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 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 = 0.4448 r_free = 0.4448 target = 0.203784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.167767 restraints weight = 12483.161| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.57 r_work: 0.3850 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4266 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= 0.143 Angle : 0.578 8.614 11696 Z= 0.328 Chirality : 0.041 0.220 1344 Planarity : 0.005 0.061 1097 Dihedral : 20.861 164.567 2227 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.53 % Favored : 94.33 % Rotamer: Outliers : 5.52 % Allowed : 27.44 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.33), residues: 705 helix: 1.48 (0.28), residues: 333 sheet: -1.66 (0.47), residues: 113 loop : -1.40 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 128 TYR 0.020 0.002 TYR B 123 PHE 0.016 0.002 PHE A 58 TRP 0.014 0.002 TRP B 342 HIS 0.004 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 8360) covalent geometry : angle 0.57798 / 0.33 (11696) hydrogen bonds : bond 0.05077 / 3.41 ( 424) hydrogen bonds : angle 4.43878 / 3.10 ( 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 180 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: A 61 LEU cc_start: 0.8368 (tt) cc_final: 0.8030 (tt) REVERT: A 106 SER cc_start: 0.7023 (t) cc_final: 0.6776 (m) REVERT: A 124 TRP cc_start: 0.5284 (OUTLIER) cc_final: 0.4192 (m-10) REVERT: A 211 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6981 (mm-30) REVERT: A 229 LEU cc_start: 0.3606 (OUTLIER) cc_final: 0.2555 (mt) REVERT: A 265 ARG cc_start: 0.6966 (ttp-170) cc_final: 0.6716 (ttp-170) REVERT: A 345 TYR cc_start: 0.4169 (OUTLIER) cc_final: 0.3406 (m-80) REVERT: B 58 PHE cc_start: 0.7318 (m-80) cc_final: 0.6793 (t80) REVERT: B 85 MET cc_start: 0.2465 (mmt) cc_final: 0.2225 (mmt) REVERT: B 118 LYS cc_start: 0.7729 (mttt) cc_final: 0.7389 (mttt) REVERT: B 124 TRP cc_start: 0.6133 (OUTLIER) cc_final: 0.5828 (m100) REVERT: B 160 PHE cc_start: 0.6322 (p90) cc_final: 0.5761 (p90) REVERT: B 170 TYR cc_start: 0.7139 (t80) cc_final: 0.6848 (t80) REVERT: B 220 LYS cc_start: 0.7770 (mttt) cc_final: 0.7472 (mttt) REVERT: B 307 LYS cc_start: 0.7003 (tppt) cc_final: 0.6736 (tppt) outliers start: 35 outliers final: 21 residues processed: 165 average time/residue: 0.1182 time to fit residues: 24.7241 Evaluate side-chains 166 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 124 TRP Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 280 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 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 124 TRP Chi-restraints excluded: chain B residue 224 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: 0.4980 chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 16 optimal weight: 0.0370 chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 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 = 0.4449 r_free = 0.4449 target = 0.206311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.170710 restraints weight = 12386.866| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.50 r_work: 0.3847 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8360 Z= 0.139 Angle : 0.575 7.851 11696 Z= 0.322 Chirality : 0.040 0.172 1344 Planarity : 0.005 0.061 1097 Dihedral : 20.843 163.838 2227 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.11 % Favored : 94.75 % Rotamer: Outliers : 5.84 % Allowed : 27.60 % Favored : 66.56 % 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: -0.05 (0.33), residues: 705 helix: 1.53 (0.27), residues: 333 sheet: -1.50 (0.48), residues: 113 loop : -1.39 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 128 TYR 0.023 0.002 TYR B 344 PHE 0.015 0.002 PHE A 96 TRP 0.016 0.002 TRP A 342 HIS 0.004 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 8360) covalent geometry : angle 0.57458 / 0.32 (11696) hydrogen bonds : bond 0.04846 / 3.24 ( 424) hydrogen bonds : angle 4.33202 / 3.05 ( 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 178 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: A 61 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8007 (tt) REVERT: A 106 SER cc_start: 0.6959 (t) cc_final: 0.6667 (m) REVERT: A 124 TRP cc_start: 0.5356 (OUTLIER) cc_final: 0.4294 (m-10) REVERT: A 187 LYS cc_start: 0.7906 (ttpp) cc_final: 0.7460 (ttpp) REVERT: A 189 ASP cc_start: 0.6847 (m-30) cc_final: 0.6149 (m-30) REVERT: A 211 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6957 (mm-30) REVERT: A 229 LEU cc_start: 0.3616 (OUTLIER) cc_final: 0.2570 (mt) REVERT: A 265 ARG cc_start: 0.7017 (ttp-170) cc_final: 0.6758 (ttp-170) REVERT: A 345 TYR cc_start: 0.3731 (OUTLIER) cc_final: 0.3029 (m-80) REVERT: B 58 PHE cc_start: 0.7272 (m-80) cc_final: 0.6822 (t80) REVERT: B 85 MET cc_start: 0.2605 (mmt) cc_final: 0.2369 (mmt) REVERT: B 118 LYS cc_start: 0.7727 (mttt) cc_final: 0.7371 (mttt) REVERT: B 160 PHE cc_start: 0.6279 (p90) cc_final: 0.5698 (p90) REVERT: B 170 TYR cc_start: 0.7184 (t80) cc_final: 0.6905 (t80) REVERT: B 183 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7563 (mt-10) REVERT: B 220 LYS cc_start: 0.7806 (mttt) cc_final: 0.7520 (mttt) REVERT: B 307 LYS cc_start: 0.7065 (tppt) cc_final: 0.6772 (tppt) outliers start: 37 outliers final: 21 residues processed: 161 average time/residue: 0.1275 time to fit residues: 26.0714 Evaluate side-chains 164 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 65 ILE 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 124 TRP Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 280 LYS 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 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 224 ILE 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: 1.9990 chunk 58 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 0.0370 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 0.0570 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** ** B 242 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 = 0.4428 r_free = 0.4428 target = 0.204312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.168694 restraints weight = 12234.156| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.51 r_work: 0.3820 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8360 Z= 0.172 Angle : 0.612 12.390 11696 Z= 0.335 Chirality : 0.043 0.373 1344 Planarity : 0.004 0.062 1097 Dihedral : 20.783 163.968 2227 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.53 % Favored : 94.33 % Rotamer: Outliers : 5.68 % Allowed : 28.39 % Favored : 65.93 % 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: 0.01 (0.33), residues: 705 helix: 1.55 (0.28), residues: 333 sheet: -1.38 (0.49), residues: 111 loop : -1.37 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 128 TYR 0.017 0.002 TYR B 123 PHE 0.017 0.002 PHE A 39 TRP 0.017 0.002 TRP A 342 HIS 0.004 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 8360) covalent geometry : angle 0.61239 / 0.34 (11696) hydrogen bonds : bond 0.04910 / 3.33 ( 424) hydrogen bonds : angle 4.31665 / 3.03 ( 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 183 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.6450 (mmt) REVERT: A 53 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: A 61 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8007 (tt) REVERT: A 106 SER cc_start: 0.6951 (t) cc_final: 0.6721 (m) REVERT: A 124 TRP cc_start: 0.5454 (OUTLIER) cc_final: 0.4327 (m-10) REVERT: A 187 LYS cc_start: 0.7888 (ttpp) cc_final: 0.7334 (ttpp) REVERT: A 189 ASP cc_start: 0.6946 (m-30) cc_final: 0.6076 (m-30) REVERT: A 211 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6896 (mm-30) REVERT: A 265 ARG cc_start: 0.7061 (ttp-170) cc_final: 0.6701 (ttp-170) REVERT: A 345 TYR cc_start: 0.3916 (OUTLIER) cc_final: 0.3229 (m-80) REVERT: B 85 MET cc_start: 0.2639 (mmt) cc_final: 0.2389 (mmt) REVERT: B 116 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7292 (t80) REVERT: B 118 LYS cc_start: 0.7751 (mttt) cc_final: 0.7394 (mttt) REVERT: B 160 PHE cc_start: 0.6277 (p90) cc_final: 0.5695 (p90) REVERT: B 170 TYR cc_start: 0.7248 (t80) cc_final: 0.6985 (t80) REVERT: B 183 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7567 (mt-10) REVERT: B 220 LYS cc_start: 0.7802 (mttt) cc_final: 0.7584 (mttt) REVERT: B 308 LEU cc_start: 0.6288 (tp) cc_final: 0.5911 (mt) outliers start: 36 outliers final: 24 residues processed: 166 average time/residue: 0.1257 time to fit residues: 26.3878 Evaluate side-chains 175 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain A residue 65 ILE 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 137 MET Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 280 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 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 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: 10.0000 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** ** B 242 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 = 0.4345 r_free = 0.4345 target = 0.193275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.159193 restraints weight = 12346.792| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.61 r_work: 0.3720 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 8360 Z= 0.329 Angle : 0.762 11.303 11696 Z= 0.419 Chirality : 0.053 0.658 1344 Planarity : 0.006 0.061 1097 Dihedral : 20.848 164.918 2227 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.38 % Favored : 93.48 % Rotamer: Outliers : 5.99 % Allowed : 28.55 % Favored : 65.46 % 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: -0.50 (0.31), residues: 705 helix: 1.05 (0.27), residues: 324 sheet: -1.37 (0.48), residues: 109 loop : -1.55 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 256 TYR 0.025 0.003 TYR A 60 PHE 0.029 0.003 PHE A 39 TRP 0.021 0.003 TRP A 124 HIS 0.006 0.002 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.33 ( 8360) covalent geometry : angle 0.76234 / 0.42 (11696) hydrogen bonds : bond 0.05948 / 4.07 ( 424) hydrogen bonds : angle 4.74088 / 3.35 ( 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 183 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.6696 (m-70) REVERT: A 53 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7963 (mt-10) REVERT: A 61 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8048 (tt) REVERT: A 106 SER cc_start: 0.7132 (t) cc_final: 0.6912 (m) REVERT: A 229 LEU cc_start: 0.4322 (OUTLIER) cc_final: 0.3247 (mt) REVERT: A 279 LYS cc_start: 0.7518 (mtpp) cc_final: 0.7254 (mtpp) REVERT: A 311 PHE cc_start: 0.7707 (t80) cc_final: 0.7278 (t80) REVERT: A 345 TYR cc_start: 0.4261 (OUTLIER) cc_final: 0.1797 (m-80) REVERT: B 53 GLU cc_start: 0.7830 (tp30) cc_final: 0.7417 (tm-30) REVERT: B 85 MET cc_start: 0.2716 (OUTLIER) cc_final: 0.2463 (mmt) REVERT: B 118 LYS cc_start: 0.7782 (mttt) cc_final: 0.7451 (mttt) REVERT: B 125 LYS cc_start: 0.7344 (mttt) cc_final: 0.7138 (tttt) REVERT: B 160 PHE cc_start: 0.6317 (p90) cc_final: 0.5774 (p90) REVERT: B 170 TYR cc_start: 0.7289 (t80) cc_final: 0.7064 (t80) REVERT: B 183 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7611 (mt-10) REVERT: B 220 LYS cc_start: 0.7818 (mttt) cc_final: 0.7584 (mttt) REVERT: B 245 THR cc_start: 0.8348 (m) cc_final: 0.8097 (t) REVERT: B 246 ILE cc_start: 0.8211 (mm) cc_final: 0.7974 (mt) REVERT: B 308 LEU cc_start: 0.6692 (tp) cc_final: 0.6314 (mt) outliers start: 38 outliers final: 21 residues processed: 167 average time/residue: 0.1116 time to fit residues: 23.7552 Evaluate side-chains 173 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 115 SER Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 280 LYS 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 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 301 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** B 242 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 = 0.4408 r_free = 0.4408 target = 0.202425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.167073 restraints weight = 12254.607| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.46 r_work: 0.3805 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8360 Z= 0.152 Angle : 0.624 10.593 11696 Z= 0.344 Chirality : 0.044 0.389 1344 Planarity : 0.005 0.060 1097 Dihedral : 20.808 164.403 2225 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.39 % Favored : 94.47 % Rotamer: Outliers : 5.05 % Allowed : 29.50 % Favored : 65.46 % 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: -0.23 (0.32), residues: 705 helix: 1.34 (0.27), residues: 330 sheet: -1.37 (0.47), residues: 109 loop : -1.51 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 256 TYR 0.026 0.002 TYR B 344 PHE 0.018 0.002 PHE A 39 TRP 0.019 0.002 TRP A 342 HIS 0.004 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 8360) covalent geometry : angle 0.62407 / 0.34 (11696) hydrogen bonds : bond 0.04986 / 3.37 ( 424) hydrogen bonds : angle 4.42376 / 3.13 ( 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 172 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7161 (mt) REVERT: A 53 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7824 (tt0) REVERT: A 61 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8073 (tt) REVERT: A 229 LEU cc_start: 0.3838 (OUTLIER) cc_final: 0.2714 (mt) REVERT: A 345 TYR cc_start: 0.3925 (OUTLIER) cc_final: 0.1895 (m-80) REVERT: B 58 PHE cc_start: 0.7541 (m-80) cc_final: 0.6710 (t80) REVERT: B 85 MET cc_start: 0.2879 (OUTLIER) cc_final: 0.2587 (mmt) REVERT: B 118 LYS cc_start: 0.7766 (mttt) cc_final: 0.7428 (mttt) REVERT: B 125 LYS cc_start: 0.7287 (mttt) cc_final: 0.7051 (tttt) REVERT: B 160 PHE cc_start: 0.6297 (p90) cc_final: 0.5747 (p90) REVERT: B 170 TYR cc_start: 0.7269 (t80) cc_final: 0.7009 (t80) REVERT: B 183 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7660 (mt-10) REVERT: B 220 LYS cc_start: 0.7767 (mttt) cc_final: 0.7549 (mttt) REVERT: B 245 THR cc_start: 0.8265 (m) cc_final: 0.7985 (t) REVERT: B 246 ILE cc_start: 0.8105 (mm) cc_final: 0.7860 (mt) outliers start: 32 outliers final: 23 residues processed: 157 average time/residue: 0.1257 time to fit residues: 25.0820 Evaluate side-chains 165 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 48 HIS 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 229 LEU Chi-restraints excluded: chain A residue 280 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 61 LEU 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 174 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 351 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 47 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 33 optimal weight: 0.0870 overall best weight: 1.6962 ------------------------------------------------------------------------------- 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** ** B 242 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 = 0.4354 r_free = 0.4354 target = 0.197568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.164220 restraints weight = 12178.801| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.55 r_work: 0.3736 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8360 Z= 0.249 Angle : 0.693 11.637 11696 Z= 0.380 Chirality : 0.047 0.425 1344 Planarity : 0.005 0.077 1097 Dihedral : 20.773 165.356 2225 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.67 % Favored : 94.18 % Rotamer: Outliers : 5.05 % Allowed : 30.60 % Favored : 64.35 % 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: -0.36 (0.31), residues: 705 helix: 1.25 (0.28), residues: 324 sheet: -1.43 (0.45), residues: 109 loop : -1.54 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 256 TYR 0.029 0.002 TYR A 123 PHE 0.025 0.003 PHE A 39 TRP 0.020 0.003 TRP A 124 HIS 0.009 0.002 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.25 ( 8360) covalent geometry : angle 0.69303 / 0.38 (11696) hydrogen bonds : bond 0.05418 / 3.69 ( 424) hydrogen bonds : angle 4.58461 / 3.24 ( 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 175 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.6966 (OUTLIER) cc_final: 0.6723 (m-70) REVERT: A 53 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7894 (mt-10) REVERT: A 61 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8086 (tt) REVERT: A 187 LYS cc_start: 0.7842 (ptmm) cc_final: 0.7625 (pttt) REVERT: A 213 GLU cc_start: 0.6498 (mm-30) cc_final: 0.6282 (mm-30) REVERT: A 229 LEU cc_start: 0.3988 (OUTLIER) cc_final: 0.2838 (mt) REVERT: A 311 PHE cc_start: 0.7620 (t80) cc_final: 0.7201 (t80) REVERT: A 345 TYR cc_start: 0.4104 (OUTLIER) cc_final: 0.1877 (m-80) REVERT: B 53 GLU cc_start: 0.7813 (tp30) cc_final: 0.7388 (tm-30) REVERT: B 58 PHE cc_start: 0.7530 (m-80) cc_final: 0.6763 (t80) REVERT: B 85 MET cc_start: 0.2867 (OUTLIER) cc_final: 0.2567 (mmt) REVERT: B 118 LYS cc_start: 0.7831 (mttt) cc_final: 0.7515 (mttt) REVERT: B 125 LYS cc_start: 0.7381 (mttt) cc_final: 0.7153 (tttt) REVERT: B 160 PHE cc_start: 0.6365 (p90) cc_final: 0.5825 (p90) REVERT: B 170 TYR cc_start: 0.7316 (t80) cc_final: 0.7078 (t80) REVERT: B 183 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7651 (mt-10) REVERT: B 220 LYS cc_start: 0.7844 (mttt) cc_final: 0.7623 (mttt) REVERT: B 241 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6650 (mtmm) REVERT: B 245 THR cc_start: 0.8287 (m) cc_final: 0.8051 (t) REVERT: B 246 ILE cc_start: 0.8174 (mm) cc_final: 0.7954 (mt) REVERT: B 308 LEU cc_start: 0.6613 (tp) cc_final: 0.6405 (mt) outliers start: 32 outliers final: 23 residues processed: 162 average time/residue: 0.1142 time to fit residues: 24.1170 Evaluate side-chains 172 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 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 46 VAL Chi-restraints excluded: chain A residue 48 HIS 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 115 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 56 LYS Chi-restraints excluded: chain B residue 61 LEU 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 174 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 351 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 5.9990 chunk 61 optimal weight: 50.0000 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** ** B 242 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 = 0.4365 r_free = 0.4365 target = 0.198581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.164027 restraints weight = 12225.159| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.32 r_work: 0.3788 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8360 Z= 0.194 Angle : 0.667 12.420 11696 Z= 0.365 Chirality : 0.045 0.355 1344 Planarity : 0.005 0.063 1097 Dihedral : 20.756 164.701 2225 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.96 % Favored : 93.90 % Rotamer: Outliers : 4.73 % Allowed : 30.76 % Favored : 64.51 % 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: -0.35 (0.31), residues: 705 helix: 1.25 (0.28), residues: 324 sheet: -1.45 (0.45), residues: 109 loop : -1.50 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 128 TYR 0.030 0.002 TYR A 123 PHE 0.022 0.002 PHE A 39 TRP 0.025 0.003 TRP B 124 HIS 0.004 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 ( 8360) covalent geometry : angle 0.66656 / 0.36 (11696) hydrogen bonds : bond 0.05058 / 3.41 ( 424) hydrogen bonds : angle 4.50462 / 3.21 ( 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 166 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7863 (mt-10) REVERT: A 61 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8174 (tt) REVERT: A 213 GLU cc_start: 0.6450 (mm-30) cc_final: 0.6158 (mm-30) REVERT: A 229 LEU cc_start: 0.3950 (OUTLIER) cc_final: 0.2766 (mt) REVERT: A 311 PHE cc_start: 0.7584 (t80) cc_final: 0.7176 (t80) REVERT: A 345 TYR cc_start: 0.3976 (OUTLIER) cc_final: 0.2098 (m-80) REVERT: B 53 GLU cc_start: 0.7781 (tp30) cc_final: 0.7334 (tm-30) REVERT: B 58 PHE cc_start: 0.7412 (m-80) cc_final: 0.6758 (t80) REVERT: B 85 MET cc_start: 0.2848 (OUTLIER) cc_final: 0.2593 (mmt) REVERT: B 116 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7291 (t80) REVERT: B 118 LYS cc_start: 0.7812 (mttt) cc_final: 0.7500 (mttt) REVERT: B 125 LYS cc_start: 0.7339 (mttt) cc_final: 0.7135 (tttt) REVERT: B 153 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 170 TYR cc_start: 0.7258 (t80) cc_final: 0.7050 (t80) REVERT: B 183 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7625 (mt-10) REVERT: B 220 LYS cc_start: 0.7852 (mttt) cc_final: 0.7609 (mttt) REVERT: B 241 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6594 (mtmm) REVERT: B 245 THR cc_start: 0.8253 (m) cc_final: 0.8037 (t) REVERT: B 246 ILE cc_start: 0.8176 (mm) cc_final: 0.7953 (mt) outliers start: 30 outliers final: 20 residues processed: 153 average time/residue: 0.1177 time to fit residues: 23.2132 Evaluate side-chains 161 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain A residue 65 ILE 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 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 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 124 TRP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 241 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 72 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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** ** B 242 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 = 0.4310 r_free = 0.4310 target = 0.188849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.153855 restraints weight = 12318.919| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.42 r_work: 0.3727 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 8360 Z= 0.308 Angle : 0.779 12.776 11696 Z= 0.424 Chirality : 0.051 0.403 1344 Planarity : 0.006 0.067 1097 Dihedral : 20.796 165.660 2225 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.10 % Favored : 93.76 % Rotamer: Outliers : 4.42 % Allowed : 30.91 % Favored : 64.67 % 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: -0.62 (0.31), residues: 705 helix: 0.91 (0.27), residues: 324 sheet: -1.18 (0.48), residues: 99 loop : -1.66 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 255 TYR 0.029 0.002 TYR A 123 PHE 0.031 0.003 PHE A 39 TRP 0.027 0.004 TRP A 124 HIS 0.006 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.31 ( 8360) covalent geometry : angle 0.77852 / 0.42 (11696) hydrogen bonds : bond 0.05834 / 3.93 ( 424) hydrogen bonds : angle 4.75375 / 3.37 ( 1157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1999.78 seconds wall clock time: 35 minutes 10.08 seconds (2110.08 seconds total)