Starting phenix.real_space_refine on Wed Feb 4 00:09:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9m_49173/02_2026/9n9m_49173_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9m_49173/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9n9m_49173/02_2026/9n9m_49173_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9m_49173/02_2026/9n9m_49173_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n9m_49173/02_2026/9n9m_49173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9m_49173/02_2026/9n9m_49173.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7995 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3016 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 357} Chain: "B" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2860 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 338} Chain breaks: 1 Chain: "a" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Classifications: {'DNA': 6} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 5} Chain: "b" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "c" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1692 Classifications: {'RNA': 79} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 42, 'rna3p_pyr': 31} Link IDs: {'rna2p': 6, 'rna3p': 72} Time building chain proxies: 1.87, per 1000 atoms: 0.23 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: 0.59 Conformation dependent library (CDL) restraints added in 158.3 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: 0.85 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: 1.12 Time building geometry restraints manager: 0.77 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=" CA GLN A 325 " pdb=" C GLN A 325 " ideal model delta sigma weight residual 1.519 1.536 -0.017 1.01e-02 9.80e+03 2.72e+00 bond pdb=" CA ASN A 132 " pdb=" CB ASN A 132 " ideal model delta sigma weight residual 1.526 1.506 0.020 1.53e-02 4.27e+03 1.69e+00 bond pdb=" C VAL B 165 " pdb=" O VAL B 165 " ideal model delta sigma weight residual 1.232 1.243 -0.010 8.90e-03 1.26e+04 1.33e+00 bond pdb=" C TYR A 233 " pdb=" O TYR A 233 " ideal model delta sigma weight residual 1.234 1.249 -0.015 1.29e-02 6.01e+03 1.29e+00 bond pdb=" CG ARG A 281 " pdb=" CD ARG A 281 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 8355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 11580 2.55 - 5.10: 99 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=" N SER B 343 " pdb=" CA SER B 343 " pdb=" C SER B 343 " ideal model delta sigma weight residual 113.19 106.76 6.43 1.58e+00 4.01e-01 1.65e+01 angle pdb=" CA LEU A 231 " pdb=" CB LEU A 231 " pdb=" CG LEU A 231 " ideal model delta sigma weight residual 116.30 129.05 -12.75 3.50e+00 8.16e-02 1.33e+01 angle pdb=" CB MET B 31 " pdb=" CG MET B 31 " pdb=" SD MET B 31 " ideal model delta sigma weight residual 112.70 123.55 -10.85 3.00e+00 1.11e-01 1.31e+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 - 0.033: 912 0.033 - 0.067: 293 0.067 - 0.100: 93 0.100 - 0.133: 41 0.133 - 0.166: 5 Chirality restraints: 1344 Sorted by residual: 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 chirality pdb=" CB VAL A 329 " pdb=" CA VAL A 329 " pdb=" CG1 VAL A 329 " pdb=" CG2 VAL A 329 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.31e-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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.160 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 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= 0.186 Angle : 0.669 12.750 11696 Z= 0.376 Chirality : 0.040 0.166 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 covalent geometry : bond 0.00377 ( 8360) covalent geometry : angle 0.66875 (11696) hydrogen bonds : bond 0.15195 ( 424) hydrogen bonds : angle 6.13300 ( 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 : 0.169 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: 0.0984 time to fit residues: 21.8322 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 : 0.162 ------------------------------------------------------------------------------- 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: 9.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN A 299 HIS ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.187832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.152612 restraints weight = 12230.355| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.48 r_work: 0.3688 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.126 8360 Z= 0.660 Angle : 1.134 13.792 11696 Z= 0.588 Chirality : 0.068 0.298 1344 Planarity : 0.008 0.077 1097 Dihedral : 21.210 167.261 2238 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.71 % Allowed : 4.96 % Favored : 94.33 % Rotamer: Outliers : 7.57 % Allowed : 24.29 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.31), residues: 705 helix: 0.19 (0.27), residues: 328 sheet: -1.63 (0.45), residues: 111 loop : -1.60 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG A 265 TYR 0.040 0.004 TYR B 123 PHE 0.045 0.005 PHE A 39 TRP 0.030 0.005 TRP A 124 HIS 0.009 0.003 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.01400 ( 8360) covalent geometry : angle 1.13385 (11696) hydrogen bonds : bond 0.08462 ( 424) hydrogen bonds : angle 5.53512 ( 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 199 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 THR cc_start: 0.8037 (m) cc_final: 0.7663 (p) REVERT: A 22 ASP cc_start: 0.6198 (OUTLIER) cc_final: 0.5982 (p0) REVERT: A 48 HIS cc_start: 0.6941 (OUTLIER) cc_final: 0.6705 (m-70) REVERT: A 62 SER cc_start: 0.8427 (m) cc_final: 0.8168 (m) REVERT: A 106 SER cc_start: 0.7229 (t) cc_final: 0.7029 (m) REVERT: A 120 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7216 (ttp-110) REVERT: A 124 TRP cc_start: 0.5853 (OUTLIER) cc_final: 0.4583 (m100) REVERT: A 189 ASP cc_start: 0.7242 (m-30) cc_final: 0.6940 (m-30) REVERT: A 211 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 265 ARG cc_start: 0.7241 (ttp-110) cc_final: 0.7025 (ttp-110) REVERT: A 352 LYS cc_start: 0.7780 (ttmt) cc_final: 0.7491 (mttt) REVERT: B 28 MET cc_start: 0.6222 (tpp) cc_final: 0.5824 (tpp) REVERT: B 53 GLU cc_start: 0.8045 (tp30) cc_final: 0.7333 (tm-30) REVERT: B 58 PHE cc_start: 0.7360 (m-80) cc_final: 0.7042 (t80) REVERT: B 113 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7164 (mt) REVERT: B 118 LYS cc_start: 0.7952 (mttt) cc_final: 0.7695 (mttt) REVERT: B 125 LYS cc_start: 0.7390 (mttt) cc_final: 0.7127 (tttt) REVERT: B 170 TYR cc_start: 0.7271 (t80) cc_final: 0.7046 (t80) REVERT: B 178 LYS cc_start: 0.8065 (mttt) cc_final: 0.7269 (mttt) REVERT: B 197 ILE cc_start: 0.7619 (mm) cc_final: 0.7389 (mm) REVERT: B 220 LYS cc_start: 0.7802 (mttt) cc_final: 0.7575 (mttt) REVERT: B 245 THR cc_start: 0.8405 (m) cc_final: 0.8039 (t) REVERT: B 308 LEU cc_start: 0.6792 (tp) cc_final: 0.6253 (mp) outliers start: 48 outliers final: 21 residues processed: 181 average time/residue: 0.1377 time to fit residues: 30.9894 Evaluate side-chains 176 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 48 HIS Chi-restraints excluded: chain A residue 60 TYR 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 120 ARG Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 236 VAL 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 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 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 113 ILE Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 301 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 132 ASN A 242 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.203313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.167583 restraints weight = 12103.946| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.46 r_work: 0.3809 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8360 Z= 0.147 Angle : 0.622 14.047 11696 Z= 0.329 Chirality : 0.042 0.451 1344 Planarity : 0.005 0.058 1097 Dihedral : 20.744 165.136 2232 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.82 % Favored : 94.75 % Rotamer: Outliers : 4.10 % Allowed : 25.71 % Favored : 70.19 % 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: -0.11 (0.32), residues: 705 helix: 1.50 (0.28), residues: 328 sheet: -1.52 (0.46), residues: 111 loop : -1.39 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.025 0.002 TYR B 123 PHE 0.017 0.002 PHE A 58 TRP 0.015 0.002 TRP A 342 HIS 0.004 0.001 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8360) covalent geometry : angle 0.62158 (11696) hydrogen bonds : bond 0.04812 ( 424) hydrogen bonds : angle 4.48737 ( 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: 26 poor density : 154 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.7211 (mm) cc_final: 0.6979 (mt) REVERT: A 22 ASP cc_start: 0.6153 (OUTLIER) cc_final: 0.5905 (p0) REVERT: A 26 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6852 (tt0) REVERT: A 53 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: A 60 TYR cc_start: 0.7887 (t80) cc_final: 0.7684 (t80) REVERT: A 123 TYR cc_start: 0.7142 (m-80) cc_final: 0.6906 (m-80) REVERT: A 160 PHE cc_start: 0.8170 (p90) cc_final: 0.7433 (p90) REVERT: A 204 ILE cc_start: 0.7805 (mt) cc_final: 0.7602 (mt) REVERT: A 345 TYR cc_start: 0.4014 (OUTLIER) cc_final: 0.3401 (m-80) REVERT: A 352 LYS cc_start: 0.7684 (ttmt) cc_final: 0.7240 (mtmt) REVERT: B 28 MET cc_start: 0.6155 (tpp) cc_final: 0.5743 (tpp) REVERT: B 53 GLU cc_start: 0.7940 (tp30) cc_final: 0.7372 (tm-30) REVERT: B 60 TYR cc_start: 0.5763 (p90) cc_final: 0.5263 (p90) REVERT: B 105 LEU cc_start: 0.7416 (mm) cc_final: 0.7063 (mp) REVERT: B 118 LYS cc_start: 0.7736 (mttt) cc_final: 0.7519 (mttt) REVERT: B 160 PHE cc_start: 0.6400 (p90) cc_final: 0.5820 (p90) REVERT: B 170 TYR cc_start: 0.7237 (t80) cc_final: 0.6959 (t80) REVERT: B 178 LYS cc_start: 0.7920 (mttt) cc_final: 0.7542 (mttt) REVERT: B 220 LYS cc_start: 0.7751 (mttt) cc_final: 0.7525 (mttt) REVERT: B 255 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.6602 (tpp80) REVERT: B 351 ILE cc_start: 0.7545 (tt) cc_final: 0.7288 (pt) REVERT: B 352 LYS cc_start: 0.8039 (mmtm) cc_final: 0.7835 (mmtm) outliers start: 26 outliers final: 12 residues processed: 169 average time/residue: 0.1318 time to fit residues: 27.9421 Evaluate side-chains 166 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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 121 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 299 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4334 r_free = 0.4334 target = 0.191172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.155904 restraints weight = 12343.411| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.36 r_work: 0.3745 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8360 Z= 0.272 Angle : 0.694 12.300 11696 Z= 0.366 Chirality : 0.046 0.377 1344 Planarity : 0.005 0.062 1097 Dihedral : 20.667 163.824 2227 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.39 % Favored : 94.33 % Rotamer: Outliers : 5.84 % Allowed : 26.81 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.32), residues: 705 helix: 1.23 (0.28), residues: 325 sheet: -1.52 (0.46), residues: 113 loop : -1.49 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 256 TYR 0.021 0.002 TYR B 123 PHE 0.030 0.002 PHE A 39 TRP 0.017 0.002 TRP A 124 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 8360) covalent geometry : angle 0.69434 (11696) hydrogen bonds : bond 0.05213 ( 424) hydrogen bonds : angle 4.62763 ( 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 189 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 THR cc_start: 0.7741 (m) cc_final: 0.7408 (p) REVERT: A 22 ASP cc_start: 0.6148 (OUTLIER) cc_final: 0.5886 (p0) REVERT: A 53 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: A 61 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 265 ARG cc_start: 0.7326 (ttp-110) cc_final: 0.6953 (ttp-170) REVERT: A 279 LYS cc_start: 0.7741 (ttpp) cc_final: 0.7506 (ttmm) REVERT: A 345 TYR cc_start: 0.4204 (OUTLIER) cc_final: 0.1776 (m-80) REVERT: A 352 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7222 (mtmt) REVERT: B 28 MET cc_start: 0.6415 (tpp) cc_final: 0.5979 (tpp) REVERT: B 53 GLU cc_start: 0.8026 (tp30) cc_final: 0.7385 (tm-30) REVERT: B 58 PHE cc_start: 0.7519 (m-80) cc_final: 0.6675 (t80) REVERT: B 118 LYS cc_start: 0.7834 (mttt) cc_final: 0.7623 (mttt) REVERT: B 124 TRP cc_start: 0.6178 (OUTLIER) cc_final: 0.5614 (m100) REVERT: B 156 LYS cc_start: 0.7518 (mtpp) cc_final: 0.7309 (mtpp) REVERT: B 170 TYR cc_start: 0.7320 (t80) cc_final: 0.7034 (t80) REVERT: B 178 LYS cc_start: 0.8007 (mttt) cc_final: 0.7628 (mttt) REVERT: B 220 LYS cc_start: 0.7792 (mttt) cc_final: 0.7531 (mttt) REVERT: B 241 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6673 (mtmm) REVERT: B 245 THR cc_start: 0.8256 (m) cc_final: 0.8019 (t) REVERT: B 308 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6568 (mt) outliers start: 37 outliers final: 19 residues processed: 169 average time/residue: 0.1123 time to fit residues: 24.3782 Evaluate side-chains 171 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 342 TRP Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 TRP 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 303 VAL 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: 0.6980 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 40 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.197460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.161649 restraints weight = 12306.758| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.50 r_work: 0.3757 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.6250 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= 0.168 Angle : 0.587 8.856 11696 Z= 0.314 Chirality : 0.041 0.192 1344 Planarity : 0.004 0.061 1097 Dihedral : 20.552 163.393 2227 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.11 % Favored : 94.61 % 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 : 0.14 % 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: -0.00 (0.32), residues: 705 helix: 1.63 (0.28), residues: 325 sheet: -1.45 (0.46), residues: 113 loop : -1.38 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 340 TYR 0.020 0.002 TYR A 60 PHE 0.017 0.002 PHE A 58 TRP 0.017 0.002 TRP A 342 HIS 0.009 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8360) covalent geometry : angle 0.58730 (11696) hydrogen bonds : bond 0.04433 ( 424) hydrogen bonds : angle 4.34601 ( 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: 35 poor density : 143 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7116 (tpp) cc_final: 0.6892 (tpp) REVERT: A 53 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: A 60 TYR cc_start: 0.8005 (t80) cc_final: 0.7752 (t80) REVERT: A 265 ARG cc_start: 0.7282 (ttp-110) cc_final: 0.6860 (ttp-170) REVERT: A 300 ARG cc_start: 0.8034 (tpp-160) cc_final: 0.7807 (tpp80) REVERT: A 345 TYR cc_start: 0.4112 (OUTLIER) cc_final: 0.3399 (m-80) REVERT: A 352 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7200 (mtmt) REVERT: B 28 MET cc_start: 0.6324 (tpp) cc_final: 0.5960 (tpp) REVERT: B 52 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: B 53 GLU cc_start: 0.7902 (tp30) cc_final: 0.7334 (tm-30) REVERT: B 58 PHE cc_start: 0.7578 (m-80) cc_final: 0.6724 (t80) REVERT: B 105 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7176 (mp) REVERT: B 118 LYS cc_start: 0.7859 (mttt) cc_final: 0.7617 (mttt) REVERT: B 156 LYS cc_start: 0.7505 (mtpp) cc_final: 0.7289 (mtpp) REVERT: B 160 PHE cc_start: 0.6467 (p90) cc_final: 0.5879 (p90) REVERT: B 170 TYR cc_start: 0.7328 (t80) cc_final: 0.7021 (t80) REVERT: B 178 LYS cc_start: 0.8024 (mttt) cc_final: 0.7708 (mttt) REVERT: B 220 LYS cc_start: 0.7814 (mttt) cc_final: 0.7550 (mttt) REVERT: B 255 ARG cc_start: 0.7869 (mmm-85) cc_final: 0.7647 (mtp180) REVERT: B 308 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6438 (mm) outliers start: 35 outliers final: 23 residues processed: 159 average time/residue: 0.1313 time to fit residues: 26.2834 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 : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 224 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 342 TRP Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 348 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.188902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.154630 restraints weight = 12403.346| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.41 r_work: 0.3708 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8360 Z= 0.225 Angle : 0.644 12.381 11696 Z= 0.342 Chirality : 0.044 0.257 1344 Planarity : 0.005 0.060 1097 Dihedral : 20.553 163.630 2227 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.53 % Favored : 94.18 % Rotamer: Outliers : 6.47 % Allowed : 26.18 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.32), residues: 705 helix: 1.47 (0.28), residues: 327 sheet: -1.41 (0.45), residues: 113 loop : -1.40 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 256 TYR 0.019 0.002 TYR A 60 PHE 0.022 0.002 PHE A 39 TRP 0.019 0.002 TRP A 342 HIS 0.006 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 8360) covalent geometry : angle 0.64404 (11696) hydrogen bonds : bond 0.04775 ( 424) hydrogen bonds : angle 4.41006 ( 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 187 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: A 265 ARG cc_start: 0.7349 (ttp-110) cc_final: 0.6986 (ttp-170) REVERT: A 274 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7367 (ttt-90) REVERT: A 311 PHE cc_start: 0.7620 (t80) cc_final: 0.7155 (t80) REVERT: A 345 TYR cc_start: 0.4209 (OUTLIER) cc_final: 0.2105 (m-80) REVERT: A 352 LYS cc_start: 0.7720 (ttmt) cc_final: 0.7282 (mtmt) REVERT: B 28 MET cc_start: 0.6441 (tpp) cc_final: 0.6050 (tpp) REVERT: B 53 GLU cc_start: 0.8015 (tp30) cc_final: 0.7406 (tm-30) REVERT: B 105 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7260 (mp) REVERT: B 118 LYS cc_start: 0.7922 (mttt) cc_final: 0.7680 (mttt) REVERT: B 156 LYS cc_start: 0.7667 (mtpp) cc_final: 0.7429 (mtpp) REVERT: B 170 TYR cc_start: 0.7347 (t80) cc_final: 0.7027 (t80) REVERT: B 178 LYS cc_start: 0.8156 (mttt) cc_final: 0.7767 (mttt) REVERT: B 220 LYS cc_start: 0.7872 (mttt) cc_final: 0.7648 (mttt) REVERT: B 241 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6615 (mtmm) REVERT: B 311 PHE cc_start: 0.8265 (t80) cc_final: 0.8053 (t80) REVERT: B 344 TYR cc_start: 0.7180 (m-80) cc_final: 0.6976 (m-80) outliers start: 41 outliers final: 24 residues processed: 165 average time/residue: 0.1202 time to fit residues: 25.3384 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 : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 211 GLU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 274 ARG 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 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 193 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.187023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.151836 restraints weight = 12389.954| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.38 r_work: 0.3700 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.7102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8360 Z= 0.273 Angle : 0.693 9.798 11696 Z= 0.367 Chirality : 0.045 0.196 1344 Planarity : 0.005 0.060 1097 Dihedral : 20.475 164.886 2227 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.67 % Favored : 94.18 % Rotamer: Outliers : 5.84 % Allowed : 28.86 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.32), residues: 705 helix: 1.23 (0.28), residues: 324 sheet: -1.15 (0.48), residues: 101 loop : -1.41 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 256 TYR 0.016 0.002 TYR A 233 PHE 0.028 0.002 PHE A 39 TRP 0.023 0.002 TRP A 342 HIS 0.007 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00576 ( 8360) covalent geometry : angle 0.69254 (11696) hydrogen bonds : bond 0.04992 ( 424) hydrogen bonds : angle 4.59501 ( 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 185 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 THR cc_start: 0.7763 (m) cc_final: 0.7370 (p) REVERT: A 123 TYR cc_start: 0.7102 (m-10) cc_final: 0.6874 (m-10) REVERT: A 265 ARG cc_start: 0.7384 (ttp-110) cc_final: 0.7010 (ttp-170) REVERT: A 274 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7354 (ttt-90) REVERT: A 311 PHE cc_start: 0.7642 (t80) cc_final: 0.7264 (t80) REVERT: A 345 TYR cc_start: 0.4142 (OUTLIER) cc_final: 0.2389 (m-80) REVERT: A 352 LYS cc_start: 0.7741 (ttmt) cc_final: 0.7321 (mtmt) REVERT: B 28 MET cc_start: 0.6470 (tpp) cc_final: 0.6071 (tpp) REVERT: B 53 GLU cc_start: 0.8016 (tp30) cc_final: 0.7682 (tp30) REVERT: B 118 LYS cc_start: 0.7949 (mttt) cc_final: 0.7718 (mttt) REVERT: B 156 LYS cc_start: 0.7821 (mtpp) cc_final: 0.7576 (mtpp) REVERT: B 170 TYR cc_start: 0.7424 (t80) cc_final: 0.7117 (t80) REVERT: B 178 LYS cc_start: 0.8183 (mttt) cc_final: 0.7775 (mttt) REVERT: B 220 LYS cc_start: 0.7876 (mttt) cc_final: 0.7619 (mttt) REVERT: B 241 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.6589 (mtmm) REVERT: B 255 ARG cc_start: 0.7973 (mmm-85) cc_final: 0.6851 (tpp80) REVERT: B 256 ARG cc_start: 0.8123 (ttt90) cc_final: 0.7880 (mtp85) REVERT: B 308 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6619 (mm) REVERT: B 314 LYS cc_start: 0.7873 (tptp) cc_final: 0.7608 (tptp) outliers start: 37 outliers final: 24 residues processed: 169 average time/residue: 0.1082 time to fit residues: 23.3848 Evaluate side-chains 174 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 48 HIS 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 211 GLU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 342 TRP Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 322 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 56 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4333 r_free = 0.4333 target = 0.191668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.156783 restraints weight = 12345.330| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.26 r_work: 0.3759 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.7193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8360 Z= 0.154 Angle : 0.601 10.090 11696 Z= 0.315 Chirality : 0.040 0.190 1344 Planarity : 0.004 0.057 1097 Dihedral : 20.367 163.695 2225 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.11 % Favored : 94.75 % Rotamer: Outliers : 4.42 % Allowed : 29.02 % 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: 0.11 (0.32), residues: 705 helix: 1.58 (0.27), residues: 326 sheet: -1.03 (0.49), residues: 101 loop : -1.31 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 184 TYR 0.021 0.001 TYR B 60 PHE 0.032 0.002 PHE B 311 TRP 0.022 0.002 TRP A 342 HIS 0.008 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8360) covalent geometry : angle 0.60086 (11696) hydrogen bonds : bond 0.04251 ( 424) hydrogen bonds : angle 4.23135 ( 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: 28 poor density : 144 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6970 (ttp-170) REVERT: A 274 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7224 (ttt-90) REVERT: A 311 PHE cc_start: 0.7540 (t80) cc_final: 0.7130 (t80) REVERT: A 345 TYR cc_start: 0.3888 (OUTLIER) cc_final: 0.3266 (m-80) REVERT: A 352 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7212 (mtmt) REVERT: B 28 MET cc_start: 0.6461 (tpp) cc_final: 0.6066 (tpp) REVERT: B 53 GLU cc_start: 0.7992 (tp30) cc_final: 0.7381 (tm-30) REVERT: B 58 PHE cc_start: 0.7499 (m-80) cc_final: 0.6784 (t80) REVERT: B 118 LYS cc_start: 0.7888 (mttt) cc_final: 0.7641 (mttt) REVERT: B 156 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7534 (mtpp) REVERT: B 160 PHE cc_start: 0.6432 (p90) cc_final: 0.5957 (p90) REVERT: B 170 TYR cc_start: 0.7380 (t80) cc_final: 0.7079 (t80) REVERT: B 178 LYS cc_start: 0.8080 (mttt) cc_final: 0.7697 (mttt) REVERT: B 220 LYS cc_start: 0.7894 (mttt) cc_final: 0.7671 (mttt) REVERT: B 255 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.6915 (tpp80) REVERT: B 256 ARG cc_start: 0.8155 (ttt90) cc_final: 0.7867 (mtp85) outliers start: 28 outliers final: 23 residues processed: 158 average time/residue: 0.1243 time to fit residues: 24.6451 Evaluate side-chains 169 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 274 ARG 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 10 ARG Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 47 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4242 r_free = 0.4242 target = 0.182485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.147321 restraints weight = 12220.396| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.43 r_work: 0.3651 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.7735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 8360 Z= 0.419 Angle : 0.841 12.744 11696 Z= 0.439 Chirality : 0.053 0.220 1344 Planarity : 0.006 0.064 1097 Dihedral : 20.549 164.524 2225 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.10 % Favored : 93.76 % Rotamer: Outliers : 5.05 % Allowed : 27.92 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.31), residues: 705 helix: 0.78 (0.27), residues: 325 sheet: -1.27 (0.48), residues: 100 loop : -1.62 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 256 TYR 0.022 0.002 TYR A 123 PHE 0.035 0.003 PHE A 39 TRP 0.028 0.003 TRP A 342 HIS 0.010 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00887 ( 8360) covalent geometry : angle 0.84117 (11696) hydrogen bonds : bond 0.05810 ( 424) hydrogen bonds : angle 4.92365 ( 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 181 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7397 (ttt-90) REVERT: A 301 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7521 (pt) REVERT: A 311 PHE cc_start: 0.7690 (t80) cc_final: 0.7330 (t80) REVERT: A 345 TYR cc_start: 0.4179 (OUTLIER) cc_final: 0.2289 (m-80) REVERT: A 352 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7398 (mtmt) REVERT: B 53 GLU cc_start: 0.8023 (tp30) cc_final: 0.7452 (tm-30) REVERT: B 112 LEU cc_start: 0.6954 (mt) cc_final: 0.6754 (mp) REVERT: B 134 LYS cc_start: 0.7367 (mtpp) cc_final: 0.7110 (mttm) REVERT: B 156 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7875 (mtpp) REVERT: B 170 TYR cc_start: 0.7517 (t80) cc_final: 0.7237 (t80) REVERT: B 178 LYS cc_start: 0.8245 (mttt) cc_final: 0.7794 (mttt) REVERT: B 220 LYS cc_start: 0.7924 (mttt) cc_final: 0.7712 (mttt) REVERT: B 232 GLU cc_start: 0.7019 (pp20) cc_final: 0.6433 (pp20) REVERT: B 255 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.6948 (tpp80) REVERT: B 344 TYR cc_start: 0.7628 (m-80) cc_final: 0.7407 (m-80) REVERT: B 350 LYS cc_start: 0.7113 (mttt) cc_final: 0.6525 (mttt) outliers start: 32 outliers final: 24 residues processed: 165 average time/residue: 0.1218 time to fit residues: 25.6690 Evaluate side-chains 173 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 342 TRP Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 4.9990 chunk 61 optimal weight: 50.0000 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 13 optimal weight: 0.4980 chunk 52 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 260 GLN A 324 ASN B 103 ASN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.188902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.154497 restraints weight = 12291.887| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.32 r_work: 0.3751 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.7732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8360 Z= 0.145 Angle : 0.633 12.845 11696 Z= 0.326 Chirality : 0.040 0.173 1344 Planarity : 0.005 0.060 1097 Dihedral : 20.350 164.607 2225 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.25 % Favored : 94.61 % Rotamer: Outliers : 3.79 % Allowed : 30.13 % Favored : 66.09 % 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 (0.31), residues: 705 helix: 1.41 (0.27), residues: 326 sheet: -0.94 (0.52), residues: 91 loop : -1.35 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 281 TYR 0.021 0.002 TYR B 123 PHE 0.030 0.002 PHE B 311 TRP 0.025 0.002 TRP A 342 HIS 0.008 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8360) covalent geometry : angle 0.63267 (11696) hydrogen bonds : bond 0.04294 ( 424) hydrogen bonds : angle 4.31153 ( 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 169 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.7859 (mtp180) cc_final: 0.7444 (mtp180) REVERT: A 153 GLU cc_start: 0.7279 (mp0) cc_final: 0.6922 (mp0) REVERT: A 244 LEU cc_start: 0.7504 (tp) cc_final: 0.7172 (tp) REVERT: A 251 GLU cc_start: 0.7134 (tt0) cc_final: 0.6726 (tt0) REVERT: A 265 ARG cc_start: 0.7284 (ttp-110) cc_final: 0.6977 (ttp-170) REVERT: A 274 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7249 (ttt-90) REVERT: A 301 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7601 (pt) REVERT: A 304 TYR cc_start: 0.8376 (m-10) cc_final: 0.7958 (m-10) REVERT: A 311 PHE cc_start: 0.7441 (t80) cc_final: 0.7001 (t80) REVERT: A 345 TYR cc_start: 0.3670 (OUTLIER) cc_final: 0.2003 (m-80) REVERT: A 352 LYS cc_start: 0.7726 (ttmt) cc_final: 0.7215 (mtmt) REVERT: B 53 GLU cc_start: 0.8007 (tp30) cc_final: 0.7407 (tm-30) REVERT: B 58 PHE cc_start: 0.7618 (m-80) cc_final: 0.6978 (t80) REVERT: B 118 LYS cc_start: 0.7777 (mttt) cc_final: 0.7461 (mttp) REVERT: B 156 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7767 (mtpp) REVERT: B 170 TYR cc_start: 0.7443 (t80) cc_final: 0.7112 (t80) REVERT: B 220 LYS cc_start: 0.7889 (mttt) cc_final: 0.7669 (mttt) REVERT: B 230 SER cc_start: 0.7965 (t) cc_final: 0.7586 (p) REVERT: B 232 GLU cc_start: 0.6854 (pp20) cc_final: 0.6267 (pp20) REVERT: B 255 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.7678 (mtp180) REVERT: B 256 ARG cc_start: 0.8146 (ttt90) cc_final: 0.7935 (mtp85) REVERT: B 350 LYS cc_start: 0.6847 (mttt) cc_final: 0.6301 (mttt) outliers start: 24 outliers final: 18 residues processed: 158 average time/residue: 0.1392 time to fit residues: 27.3605 Evaluate side-chains 162 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 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 251 GLU Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4270 r_free = 0.4270 target = 0.184223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.149601 restraints weight = 12325.150| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.36 r_work: 0.3685 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.7888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8360 Z= 0.307 Angle : 0.741 10.989 11696 Z= 0.387 Chirality : 0.047 0.236 1344 Planarity : 0.006 0.061 1097 Dihedral : 20.386 164.117 2225 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.52 % Favored : 93.33 % Rotamer: Outliers : 3.63 % Allowed : 30.13 % Favored : 66.25 % 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: -0.46 (0.31), residues: 705 helix: 1.04 (0.27), residues: 325 sheet: -1.31 (0.50), residues: 99 loop : -1.50 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 256 TYR 0.015 0.002 TYR A 123 PHE 0.031 0.003 PHE A 116 TRP 0.083 0.004 TRP A 342 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 8360) covalent geometry : angle 0.74111 (11696) hydrogen bonds : bond 0.04988 ( 424) hydrogen bonds : angle 4.67560 ( 1157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1951.22 seconds wall clock time: 34 minutes 14.29 seconds (2054.29 seconds total)