Starting phenix.real_space_refine on Wed Aug 5 02:46:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9o_49174/08_2026/9n9o_49174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9o_49174/08_2026/9n9o_49174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n9o_49174/08_2026/9n9o_49174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9o_49174/08_2026/9n9o_49174_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n9o_49174/08_2026/9n9o_49174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9o_49174/08_2026/9n9o_49174.map" } resolution = 3.42 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= 0.030 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 109 5.49 5 S 30 5.16 5 C 4823 2.51 5 N 1463 2.21 5 O 1760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8185 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: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "c" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1777 Classifications: {'RNA': 83} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 44, 'rna3p_pyr': 33} Link IDs: {'rna2p': 6, 'rna3p': 76} Time building chain proxies: 1.55, per 1000 atoms: 0.19 Number of scatterers: 8185 At special positions: 0 Unit cell: (107.682, 103.572, 88.776, 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 109 15.00 O 1760 8.00 N 1463 7.00 C 4823 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: 0.70 Conformation dependent library (CDL) restraints added in 126.7 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: 23 helices and 6 sheets defined 51.9% alpha, 21.4% beta 39 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 20 through 64 removed outlier: 4.060A pdb=" N GLN A 52 " --> pdb=" O HIS A 48 " (cutoff:3.500A) removed outlier: 4.136A 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: 4.156A pdb=" N LEU A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.677A 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 146 Processing helix chain 'A' and resid 178 through 187 removed outlier: 3.546A pdb=" N LYS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 270 removed outlier: 3.637A pdb=" N TYR A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.603A pdb=" N LYS A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 291 through 315 Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 335 through 342 removed outlier: 3.517A pdb=" N LEU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 359 removed outlier: 3.565A pdb=" N LEU A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) 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: 4.386A pdb=" N THR B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 125 removed outlier: 5.323A pdb=" N VAL B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 248 through 272 removed outlier: 4.496A pdb=" N ARG B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 315 removed outlier: 5.812A pdb=" N ALA B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL B 286 " --> pdb=" O LYS B 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS B 315 " --> pdb=" O PHE B 311 " (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 140 removed outlier: 4.355A pdb=" N VAL A 209 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N SER A 195 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 207 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE A 197 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE A 205 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 204 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE A 158 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 157 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A 152 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 71 removed outlier: 8.258A pdb=" N LYS A 68 " --> pdb=" O ILE A 79 " (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: 4.472A pdb=" N THR A 319 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 223 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE A 321 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA A 225 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.550A pdb=" N PHE B 141 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B 204 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 208 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN B 13 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N PHE B 158 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA B 157 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TYR B 151 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N CYS B 159 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.429A 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: 3.550A pdb=" N PHE B 141 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 242 through 246 removed outlier: 3.639A pdb=" N LEU B 244 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR B 319 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL B 223 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE B 321 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA B 225 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 322 " --> pdb=" O ILE B 363 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1944 1.33 - 1.45: 2293 1.45 - 1.57: 4069 1.57 - 1.69: 215 1.69 - 1.82: 52 Bond restraints: 8573 Sorted by residual: bond pdb=" C3' DC b -7 " pdb=" O3' DC b -7 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 9.14e+00 bond pdb=" C3' DA a -3 " pdb=" C2' DA a -3 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.08e+00 bond pdb=" O4' DC b -5 " pdb=" C1' DC b -5 " ideal model delta sigma weight residual 1.420 1.388 0.032 1.10e-02 8.26e+03 8.45e+00 bond pdb=" N1 DC b -7 " pdb=" C6 DC b -7 " ideal model delta sigma weight residual 1.367 1.351 0.016 6.00e-03 2.78e+04 7.12e+00 bond pdb=" C3' DG a -2 " pdb=" C2' DG a -2 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.88e+00 ... (remaining 8568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 11553 2.03 - 4.06: 440 4.06 - 6.08: 27 6.08 - 8.11: 5 8.11 - 10.14: 2 Bond angle restraints: 12027 Sorted by residual: angle pdb=" CA ARG A 265 " pdb=" CB ARG A 265 " pdb=" CG ARG A 265 " ideal model delta sigma weight residual 114.10 123.87 -9.77 2.00e+00 2.50e-01 2.39e+01 angle pdb=" C1' C c 47 " pdb=" N1 C c 47 " pdb=" C2 C c 47 " ideal model delta sigma weight residual 118.80 124.16 -5.36 1.10e+00 8.26e-01 2.38e+01 angle pdb=" C1' C c 13 " pdb=" N1 C c 13 " pdb=" C2 C c 13 " ideal model delta sigma weight residual 118.80 123.80 -5.00 1.10e+00 8.26e-01 2.07e+01 angle pdb=" O5' G c 29 " pdb=" C5' G c 29 " pdb=" C4' G c 29 " ideal model delta sigma weight residual 109.40 112.85 -3.45 8.00e-01 1.56e+00 1.86e+01 angle pdb=" O5' A c 73 " pdb=" C5' A c 73 " pdb=" C4' A c 73 " ideal model delta sigma weight residual 109.40 112.72 -3.32 8.00e-01 1.56e+00 1.72e+01 ... (remaining 12022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.08: 4756 33.08 - 66.15: 425 66.15 - 99.23: 26 99.23 - 132.30: 0 132.30 - 165.38: 1 Dihedral angle restraints: 5208 sinusoidal: 3123 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 34.62 165.38 1 1.50e+01 4.44e-03 8.40e+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 -110.09 -49.91 1 1.50e+01 4.44e-03 1.52e+01 dihedral pdb=" O4' U c 75 " pdb=" C1' U c 75 " pdb=" N1 U c 75 " pdb=" C2 U c 75 " ideal model delta sinusoidal sigma weight residual -128.00 -72.64 -55.36 1 1.70e+01 3.46e-03 1.43e+01 ... (remaining 5205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 899 0.040 - 0.080: 283 0.080 - 0.120: 121 0.120 - 0.160: 79 0.160 - 0.200: 2 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CA GLU B 232 " pdb=" N GLU B 232 " pdb=" C GLU B 232 " pdb=" CB GLU B 232 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CB THR A 349 " pdb=" CA THR A 349 " pdb=" OG1 THR A 349 " pdb=" CG2 THR A 349 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" C3' DA b -2 " pdb=" C4' DA b -2 " pdb=" O3' DA b -2 " pdb=" C2' DA b -2 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 1381 not shown) Planarity restraints: 1106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G c 28 " 0.046 2.00e-02 2.50e+03 1.92e-02 1.11e+01 pdb=" N9 G c 28 " -0.044 2.00e-02 2.50e+03 pdb=" C8 G c 28 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G c 28 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G c 28 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G c 28 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G c 28 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G c 28 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G c 28 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G c 28 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G c 28 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G c 28 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 233 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO B 234 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 254 " 0.015 2.00e-02 2.50e+03 1.40e-02 3.89e+00 pdb=" CG TYR B 254 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 254 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 254 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 254 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 254 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 254 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 254 " 0.001 2.00e-02 2.50e+03 ... (remaining 1103 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 309 2.68 - 3.24: 7582 3.24 - 3.79: 14419 3.79 - 4.35: 18343 4.35 - 4.90: 27737 Nonbonded interactions: 68390 Sorted by model distance: nonbonded pdb=" O ARG A 84 " pdb=" OG1 THR A 87 " model vdw 2.129 3.040 nonbonded pdb=" OE2 GLU A 336 " pdb=" O2' U c 83 " model vdw 2.137 3.040 nonbonded pdb=" OD1 ASN B 341 " pdb=" N TRP B 342 " model vdw 2.184 3.120 nonbonded pdb=" O ARG A 340 " pdb=" NH1 ARG A 340 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR A 88 " pdb=" OD1 ASN A 109 " model vdw 2.257 3.040 ... (remaining 68385 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: 1.130 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 7.610 Find NCS groups from input model: 0.070 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8573 Z= 0.403 Angle : 0.783 10.139 12027 Z= 0.566 Chirality : 0.053 0.200 1384 Planarity : 0.004 0.052 1106 Dihedral : 20.636 165.379 3866 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer: Outliers : 3.31 % Allowed : 31.07 % Favored : 65.62 % 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: 0.11 (0.32), residues: 705 helix: 1.23 (0.28), residues: 333 sheet: -0.58 (0.48), residues: 114 loop : -1.08 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 265 TYR 0.034 0.002 TYR B 254 PHE 0.022 0.002 PHE A 39 TRP 0.019 0.002 TRP B 342 HIS 0.003 0.001 HIS A 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.40 ( 8573) covalent geometry : angle 0.78294 / 0.57 (12027) hydrogen bonds : bond 0.15175 / 10.01 ( 430) hydrogen bonds : angle 5.86515 / 4.11 ( 1153) *********************** 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 155 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.5703 (mm-30) cc_final: 0.5393 (mm-30) REVERT: A 123 TYR cc_start: 0.5870 (m-80) cc_final: 0.5406 (m-80) REVERT: A 193 CYS cc_start: 0.7892 (m) cc_final: 0.7570 (m) REVERT: B 15 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5953 (mt) REVERT: B 25 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7541 (mmmm) REVERT: B 30 MET cc_start: 0.6624 (ttt) cc_final: 0.6351 (ttt) REVERT: B 57 ASP cc_start: 0.7232 (t0) cc_final: 0.6840 (t0) REVERT: B 124 TRP cc_start: 0.5602 (OUTLIER) cc_final: 0.5226 (m100) REVERT: B 187 LYS cc_start: 0.8317 (mttt) cc_final: 0.7968 (mttt) REVERT: B 255 ARG cc_start: 0.7530 (mmm-85) cc_final: 0.7310 (ttt180) outliers start: 21 outliers final: 6 residues processed: 150 average time/residue: 0.1109 time to fit residues: 21.6822 Evaluate side-chains 132 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 15 LEU Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 40.0000 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 299 HIS B 103 ASN B 242 ASN B 299 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.210905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.174240 restraints weight = 12869.846| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.29 r_work: 0.3903 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 8573 Z= 0.341 Angle : 0.856 10.504 12027 Z= 0.465 Chirality : 0.054 0.335 1384 Planarity : 0.007 0.069 1106 Dihedral : 20.510 165.133 2352 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.97 % Favored : 95.89 % Rotamer: Outliers : 6.15 % Allowed : 27.13 % 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: -0.89 (0.30), residues: 705 helix: 0.23 (0.25), residues: 345 sheet: -0.82 (0.48), residues: 124 loop : -1.54 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 265 TYR 0.033 0.003 TYR B 254 PHE 0.032 0.003 PHE A 39 TRP 0.025 0.004 TRP B 34 HIS 0.013 0.002 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.34 ( 8573) covalent geometry : angle 0.85613 / 0.47 (12027) hydrogen bonds : bond 0.06733 / 4.56 ( 430) hydrogen bonds : angle 4.94281 / 3.60 ( 1153) *********************** 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 175 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7638 (pt) REVERT: A 193 CYS cc_start: 0.8063 (m) cc_final: 0.7851 (m) REVERT: A 196 ASN cc_start: 0.7443 (m-40) cc_final: 0.7179 (m-40) REVERT: A 266 THR cc_start: 0.7541 (m) cc_final: 0.7234 (p) REVERT: A 273 SER cc_start: 0.7424 (m) cc_final: 0.7206 (p) REVERT: A 277 LYS cc_start: 0.7214 (tptt) cc_final: 0.6882 (tptt) REVERT: A 302 HIS cc_start: 0.7005 (OUTLIER) cc_final: 0.5155 (m-70) REVERT: A 303 VAL cc_start: 0.7438 (m) cc_final: 0.7222 (t) REVERT: A 323 MET cc_start: 0.6706 (mmm) cc_final: 0.6408 (mmm) REVERT: B 54 MET cc_start: 0.6879 (mmm) cc_final: 0.6407 (mmt) REVERT: B 57 ASP cc_start: 0.7689 (t0) cc_final: 0.7195 (t0) REVERT: B 119 ASN cc_start: 0.6764 (m110) cc_final: 0.6405 (m-40) REVERT: B 125 LYS cc_start: 0.7834 (mttt) cc_final: 0.7530 (mttt) REVERT: B 168 LYS cc_start: 0.6999 (pttt) cc_final: 0.6650 (pttt) REVERT: B 232 GLU cc_start: 0.5052 (pp20) cc_final: 0.4734 (pp20) REVERT: B 295 ASN cc_start: 0.7196 (t0) cc_final: 0.6740 (t0) REVERT: B 313 ILE cc_start: 0.7280 (mp) cc_final: 0.7034 (mp) REVERT: B 325 GLN cc_start: 0.3711 (OUTLIER) cc_final: 0.3218 (tm-30) REVERT: B 339 LEU cc_start: 0.3272 (mm) cc_final: 0.2885 (mt) outliers start: 39 outliers final: 16 residues processed: 168 average time/residue: 0.0962 time to fit residues: 21.1119 Evaluate side-chains 152 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 101 PRO Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 50.0000 chunk 79 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.211348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.173768 restraints weight = 12647.847| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.29 r_work: 0.3905 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8573 Z= 0.214 Angle : 0.625 7.341 12027 Z= 0.354 Chirality : 0.043 0.203 1384 Planarity : 0.005 0.053 1106 Dihedral : 20.319 165.580 2343 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 5.68 % Allowed : 25.87 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.31), residues: 705 helix: 0.87 (0.27), residues: 344 sheet: -1.02 (0.48), residues: 123 loop : -1.38 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 40 TYR 0.018 0.002 TYR B 254 PHE 0.023 0.002 PHE A 39 TRP 0.012 0.001 TRP B 34 HIS 0.004 0.002 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 ( 8573) covalent geometry : angle 0.62508 / 0.35 (12027) hydrogen bonds : bond 0.05193 / 3.47 ( 430) hydrogen bonds : angle 4.61596 / 3.34 ( 1153) *********************** 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 173 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7868 (mmt180) REVERT: A 45 ILE cc_start: 0.7746 (mm) cc_final: 0.7532 (mt) REVERT: A 65 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7698 (pt) REVERT: A 148 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7708 (mtt90) REVERT: A 196 ASN cc_start: 0.7566 (m-40) cc_final: 0.7245 (m-40) REVERT: A 248 THR cc_start: 0.6537 (OUTLIER) cc_final: 0.6055 (m) REVERT: A 266 THR cc_start: 0.7467 (m) cc_final: 0.7165 (p) REVERT: A 277 LYS cc_start: 0.7399 (tptt) cc_final: 0.7124 (tptt) REVERT: A 302 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.4375 (m170) REVERT: A 303 VAL cc_start: 0.7483 (m) cc_final: 0.7262 (t) REVERT: A 323 MET cc_start: 0.6655 (mmm) cc_final: 0.6371 (mmm) REVERT: B 15 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5738 (tt) REVERT: B 25 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7463 (mmmm) REVERT: B 54 MET cc_start: 0.6830 (mmm) cc_final: 0.6406 (mmt) REVERT: B 57 ASP cc_start: 0.7740 (t0) cc_final: 0.7402 (t0) REVERT: B 100 MET cc_start: 0.5934 (tpt) cc_final: 0.5475 (tpt) REVERT: B 125 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7596 (mttt) REVERT: B 168 LYS cc_start: 0.6865 (pttt) cc_final: 0.6412 (mtmm) REVERT: B 187 LYS cc_start: 0.8224 (mttt) cc_final: 0.7825 (mttt) REVERT: B 295 ASN cc_start: 0.7340 (t0) cc_final: 0.6991 (t0) REVERT: B 313 ILE cc_start: 0.7302 (mp) cc_final: 0.7041 (mp) REVERT: B 325 GLN cc_start: 0.3617 (OUTLIER) cc_final: 0.2410 (tm-30) REVERT: B 339 LEU cc_start: 0.3264 (mm) cc_final: 0.2819 (mt) REVERT: B 346 GLU cc_start: 0.7217 (mp0) cc_final: 0.6848 (mp0) outliers start: 36 outliers final: 15 residues processed: 160 average time/residue: 0.1168 time to fit residues: 24.0168 Evaluate side-chains 158 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG 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 150 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 364 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 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 = 0.4480 r_free = 0.4480 target = 0.209961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.174044 restraints weight = 12910.898| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.30 r_work: 0.3861 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8573 Z= 0.178 Angle : 0.580 8.470 12027 Z= 0.329 Chirality : 0.040 0.226 1384 Planarity : 0.005 0.056 1106 Dihedral : 20.292 163.558 2343 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.88 % Rotamer: Outliers : 5.52 % Allowed : 25.55 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.32), residues: 705 helix: 1.09 (0.27), residues: 343 sheet: -1.19 (0.48), residues: 123 loop : -1.25 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 40 TYR 0.017 0.002 TYR B 60 PHE 0.020 0.002 PHE B 116 TRP 0.011 0.001 TRP B 34 HIS 0.005 0.002 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 ( 8573) covalent geometry : angle 0.58013 / 0.33 (12027) hydrogen bonds : bond 0.04760 / 3.18 ( 430) hydrogen bonds : angle 4.50990 / 3.26 ( 1153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8054 (mmm-85) REVERT: A 45 ILE cc_start: 0.7726 (mm) cc_final: 0.7497 (mt) REVERT: A 54 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6827 (ttm) REVERT: A 65 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7804 (pt) REVERT: A 196 ASN cc_start: 0.7571 (m-40) cc_final: 0.7248 (m-40) REVERT: A 248 THR cc_start: 0.6570 (OUTLIER) cc_final: 0.6060 (m) REVERT: A 266 THR cc_start: 0.7521 (m) cc_final: 0.7264 (p) REVERT: A 277 LYS cc_start: 0.7481 (tptt) cc_final: 0.7014 (tppp) REVERT: A 302 HIS cc_start: 0.7139 (OUTLIER) cc_final: 0.5711 (m-70) REVERT: A 303 VAL cc_start: 0.7572 (m) cc_final: 0.7330 (t) REVERT: B 15 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5744 (tt) REVERT: B 25 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7425 (mmmm) REVERT: B 54 MET cc_start: 0.6876 (mmm) cc_final: 0.6509 (mmt) REVERT: B 57 ASP cc_start: 0.7847 (t0) cc_final: 0.7457 (t0) REVERT: B 125 LYS cc_start: 0.7857 (mttt) cc_final: 0.7632 (mttt) REVERT: B 168 LYS cc_start: 0.6868 (pttt) cc_final: 0.6370 (mtmm) REVERT: B 187 LYS cc_start: 0.8229 (mttt) cc_final: 0.7767 (mttt) REVERT: B 264 ARG cc_start: 0.6454 (mtm110) cc_final: 0.6144 (mtm110) REVERT: B 295 ASN cc_start: 0.7584 (t0) cc_final: 0.7323 (t0) REVERT: B 313 ILE cc_start: 0.7242 (mp) cc_final: 0.6973 (mp) REVERT: B 325 GLN cc_start: 0.2861 (OUTLIER) cc_final: 0.2498 (tm-30) REVERT: B 339 LEU cc_start: 0.3496 (mm) cc_final: 0.2990 (mt) REVERT: B 346 GLU cc_start: 0.7197 (mp0) cc_final: 0.6364 (mp0) outliers start: 35 outliers final: 18 residues processed: 160 average time/residue: 0.1138 time to fit residues: 23.5074 Evaluate side-chains 160 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 0.0470 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** 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 = 0.4485 r_free = 0.4485 target = 0.210266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.174412 restraints weight = 12732.600| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.30 r_work: 0.3868 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8573 Z= 0.145 Angle : 0.543 7.557 12027 Z= 0.307 Chirality : 0.038 0.210 1384 Planarity : 0.004 0.053 1106 Dihedral : 20.285 162.329 2343 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.60 % Rotamer: Outliers : 5.21 % Allowed : 26.81 % Favored : 67.98 % 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: -0.08 (0.32), residues: 705 helix: 1.24 (0.27), residues: 345 sheet: -1.19 (0.47), residues: 123 loop : -1.27 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 263 TYR 0.019 0.001 TYR B 60 PHE 0.026 0.002 PHE B 116 TRP 0.014 0.002 TRP B 342 HIS 0.010 0.002 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 ( 8573) covalent geometry : angle 0.54302 / 0.31 (12027) hydrogen bonds : bond 0.04479 / 2.97 ( 430) hydrogen bonds : angle 4.29555 / 3.09 ( 1153) *********************** 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 167 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.7048 (mmm) cc_final: 0.6702 (tpp) REVERT: A 196 ASN cc_start: 0.7579 (m-40) cc_final: 0.7265 (m-40) REVERT: A 211 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6602 (mm-30) REVERT: A 248 THR cc_start: 0.6605 (OUTLIER) cc_final: 0.6170 (m) REVERT: A 250 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6545 (tm-30) REVERT: A 266 THR cc_start: 0.7518 (m) cc_final: 0.7257 (p) REVERT: A 277 LYS cc_start: 0.7580 (tptt) cc_final: 0.7055 (mmmm) REVERT: A 302 HIS cc_start: 0.7139 (OUTLIER) cc_final: 0.5754 (m-70) REVERT: A 303 VAL cc_start: 0.7544 (m) cc_final: 0.7260 (t) REVERT: B 15 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5681 (tt) REVERT: B 54 MET cc_start: 0.6771 (mmm) cc_final: 0.6438 (mmt) REVERT: B 57 ASP cc_start: 0.7835 (t0) cc_final: 0.7429 (t0) REVERT: B 100 MET cc_start: 0.5390 (tpt) cc_final: 0.5072 (tpt) REVERT: B 125 LYS cc_start: 0.7857 (mttt) cc_final: 0.7620 (mttt) REVERT: B 168 LYS cc_start: 0.6880 (pttt) cc_final: 0.6373 (mtmm) REVERT: B 264 ARG cc_start: 0.6401 (mtm110) cc_final: 0.6096 (mtm110) REVERT: B 313 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6955 (mp) REVERT: B 325 GLN cc_start: 0.2838 (OUTLIER) cc_final: 0.2481 (tm-30) REVERT: B 339 LEU cc_start: 0.3558 (mm) cc_final: 0.3043 (mt) REVERT: B 346 GLU cc_start: 0.7302 (mp0) cc_final: 0.7097 (mp0) outliers start: 33 outliers final: 21 residues processed: 153 average time/residue: 0.1073 time to fit residues: 21.1930 Evaluate side-chains 154 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 364 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 30.0000 chunk 3 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.208303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.172161 restraints weight = 12471.977| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.27 r_work: 0.3835 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8573 Z= 0.178 Angle : 0.590 10.618 12027 Z= 0.324 Chirality : 0.040 0.234 1384 Planarity : 0.004 0.048 1106 Dihedral : 20.274 162.131 2343 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.60 % 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 : 0.00 % 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: -0.16 (0.32), residues: 705 helix: 1.14 (0.27), residues: 344 sheet: -1.24 (0.47), residues: 123 loop : -1.23 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 40 TYR 0.019 0.002 TYR B 60 PHE 0.021 0.002 PHE A 39 TRP 0.014 0.002 TRP B 34 HIS 0.007 0.002 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 ( 8573) covalent geometry : angle 0.58975 / 0.32 (12027) hydrogen bonds : bond 0.04628 / 3.08 ( 430) hydrogen bonds : angle 4.26281 / 3.07 ( 1153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8037 (mmm-85) REVERT: A 30 MET cc_start: 0.6925 (ttm) cc_final: 0.6709 (ttt) REVERT: A 56 LYS cc_start: 0.7892 (ttpp) cc_final: 0.7547 (ttpp) REVERT: A 187 LYS cc_start: 0.7468 (ptmt) cc_final: 0.7243 (ptmt) REVERT: A 196 ASN cc_start: 0.7642 (m-40) cc_final: 0.7291 (m-40) REVERT: A 248 THR cc_start: 0.6831 (OUTLIER) cc_final: 0.6294 (m) REVERT: A 250 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6734 (tm-30) REVERT: A 251 GLU cc_start: 0.6620 (tt0) cc_final: 0.6376 (tt0) REVERT: A 259 ILE cc_start: 0.6562 (mt) cc_final: 0.6331 (tt) REVERT: A 266 THR cc_start: 0.7523 (m) cc_final: 0.7294 (p) REVERT: A 277 LYS cc_start: 0.7732 (tptt) cc_final: 0.7181 (mmmm) REVERT: A 302 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.5648 (m-70) REVERT: A 303 VAL cc_start: 0.7573 (m) cc_final: 0.7325 (t) REVERT: B 15 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5724 (tt) REVERT: B 25 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7406 (mmmm) REVERT: B 57 ASP cc_start: 0.7862 (t0) cc_final: 0.7488 (t0) REVERT: B 100 MET cc_start: 0.5482 (tpt) cc_final: 0.5049 (tpt) REVERT: B 119 ASN cc_start: 0.6713 (m110) cc_final: 0.6248 (m-40) REVERT: B 168 LYS cc_start: 0.6945 (pttt) cc_final: 0.6444 (mtmm) REVERT: B 187 LYS cc_start: 0.8196 (mttt) cc_final: 0.7734 (mttt) REVERT: B 220 LYS cc_start: 0.7653 (mttt) cc_final: 0.7365 (mttt) REVERT: B 264 ARG cc_start: 0.6316 (mtm110) cc_final: 0.5896 (mtm110) REVERT: B 313 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6938 (mp) REVERT: B 323 MET cc_start: 0.6739 (mmm) cc_final: 0.6404 (mmm) REVERT: B 325 GLN cc_start: 0.2953 (OUTLIER) cc_final: 0.2558 (tm-30) REVERT: B 339 LEU cc_start: 0.3922 (mm) cc_final: 0.3235 (mt) outliers start: 41 outliers final: 24 residues processed: 161 average time/residue: 0.0995 time to fit residues: 20.5413 Evaluate side-chains 163 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG 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 67 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 364 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 65 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 61 optimal weight: 40.0000 chunk 24 optimal weight: 0.0070 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** 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 = 0.4429 r_free = 0.4429 target = 0.205052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.167209 restraints weight = 12675.789| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.24 r_work: 0.3785 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8573 Z= 0.233 Angle : 0.660 11.026 12027 Z= 0.363 Chirality : 0.044 0.236 1384 Planarity : 0.006 0.069 1106 Dihedral : 20.352 163.557 2343 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.68 % Favored : 95.18 % Rotamer: Outliers : 5.99 % Allowed : 27.29 % 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: -0.44 (0.32), residues: 705 helix: 0.86 (0.27), residues: 344 sheet: -1.35 (0.46), residues: 123 loop : -1.29 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 40 TYR 0.019 0.002 TYR B 60 PHE 0.022 0.002 PHE A 39 TRP 0.038 0.003 TRP A 124 HIS 0.011 0.002 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 ( 8573) covalent geometry : angle 0.65976 / 0.36 (12027) hydrogen bonds : bond 0.05262 / 3.48 ( 430) hydrogen bonds : angle 4.58304 / 3.31 ( 1153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8129 (mmm-85) REVERT: A 28 MET cc_start: 0.8090 (mmm) cc_final: 0.7547 (mmt) REVERT: A 30 MET cc_start: 0.6990 (ttm) cc_final: 0.6741 (ttt) REVERT: A 248 THR cc_start: 0.7067 (OUTLIER) cc_final: 0.6542 (m) REVERT: A 250 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6806 (tm-30) REVERT: A 266 THR cc_start: 0.7543 (m) cc_final: 0.7303 (p) REVERT: A 274 ARG cc_start: 0.7727 (tpt170) cc_final: 0.7032 (tpt170) REVERT: A 277 LYS cc_start: 0.7916 (tptt) cc_final: 0.7403 (mmmm) REVERT: A 280 LYS cc_start: 0.5400 (mttp) cc_final: 0.4931 (mttp) REVERT: A 302 HIS cc_start: 0.7168 (OUTLIER) cc_final: 0.5346 (m-70) REVERT: B 25 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7436 (mmmm) REVERT: B 100 MET cc_start: 0.5689 (tpt) cc_final: 0.5264 (tpt) REVERT: B 168 LYS cc_start: 0.6953 (pttt) cc_final: 0.6499 (mtmm) REVERT: B 264 ARG cc_start: 0.6423 (mtm110) cc_final: 0.5904 (mtm110) REVERT: B 313 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.7070 (mp) REVERT: B 323 MET cc_start: 0.6773 (mmm) cc_final: 0.6440 (mmm) REVERT: B 325 GLN cc_start: 0.3329 (OUTLIER) cc_final: 0.2906 (tm-30) outliers start: 38 outliers final: 23 residues processed: 159 average time/residue: 0.1139 time to fit residues: 23.1883 Evaluate side-chains 160 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG 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 67 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 364 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 40.0000 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.0670 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 30.0000 chunk 74 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.203256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.165380 restraints weight = 12494.006| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.19 r_work: 0.3763 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8573 Z= 0.254 Angle : 0.662 9.584 12027 Z= 0.364 Chirality : 0.044 0.223 1384 Planarity : 0.005 0.066 1106 Dihedral : 20.452 164.391 2343 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.26 % Favored : 95.60 % Rotamer: Outliers : 5.84 % Allowed : 27.29 % Favored : 66.88 % 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: -0.58 (0.31), residues: 705 helix: 0.73 (0.26), residues: 343 sheet: -1.46 (0.46), residues: 123 loop : -1.28 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 40 TYR 0.021 0.002 TYR A 123 PHE 0.026 0.002 PHE A 139 TRP 0.025 0.003 TRP A 124 HIS 0.007 0.002 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 ( 8573) covalent geometry : angle 0.66202 / 0.36 (12027) hydrogen bonds : bond 0.05280 / 3.49 ( 430) hydrogen bonds : angle 4.60317 / 3.29 ( 1153) *********************** 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 169 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8001 (mmm-85) REVERT: A 248 THR cc_start: 0.7205 (OUTLIER) cc_final: 0.6723 (m) REVERT: A 266 THR cc_start: 0.7577 (m) cc_final: 0.7354 (p) REVERT: A 277 LYS cc_start: 0.7927 (tptt) cc_final: 0.7359 (mmmm) REVERT: B 25 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7165 (mmmm) REVERT: B 100 MET cc_start: 0.5741 (tpt) cc_final: 0.5359 (tpt) REVERT: B 119 ASN cc_start: 0.6793 (m110) cc_final: 0.6328 (m-40) REVERT: B 168 LYS cc_start: 0.6976 (pttt) cc_final: 0.6530 (mtmt) REVERT: B 264 ARG cc_start: 0.6358 (mtm110) cc_final: 0.5835 (mtm110) REVERT: B 313 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7068 (mp) REVERT: B 325 GLN cc_start: 0.3353 (OUTLIER) cc_final: 0.2935 (tm-30) outliers start: 37 outliers final: 23 residues processed: 154 average time/residue: 0.1038 time to fit residues: 20.5159 Evaluate side-chains 159 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 364 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 11 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.205775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.167518 restraints weight = 12533.647| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.24 r_work: 0.3799 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8573 Z= 0.147 Angle : 0.592 10.448 12027 Z= 0.326 Chirality : 0.040 0.202 1384 Planarity : 0.005 0.052 1106 Dihedral : 20.465 162.799 2341 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer: Outliers : 4.42 % Allowed : 29.18 % Favored : 66.40 % 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: -0.34 (0.31), residues: 705 helix: 1.07 (0.27), residues: 345 sheet: -1.45 (0.46), residues: 123 loop : -1.38 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 40 TYR 0.018 0.001 TYR B 60 PHE 0.021 0.002 PHE A 139 TRP 0.024 0.003 TRP B 342 HIS 0.005 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 8573) covalent geometry : angle 0.59174 / 0.33 (12027) hydrogen bonds : bond 0.04710 / 3.09 ( 430) hydrogen bonds : angle 4.37167 / 3.13 ( 1153) *********************** 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 164 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8075 (mmm-85) REVERT: A 196 ASN cc_start: 0.7708 (m-40) cc_final: 0.7404 (m-40) REVERT: A 248 THR cc_start: 0.7142 (OUTLIER) cc_final: 0.6770 (m) REVERT: A 259 ILE cc_start: 0.7289 (mt) cc_final: 0.6926 (tt) REVERT: A 266 THR cc_start: 0.7589 (m) cc_final: 0.7334 (p) REVERT: A 277 LYS cc_start: 0.7982 (tptt) cc_final: 0.7339 (mmmm) REVERT: B 57 ASP cc_start: 0.7586 (t0) cc_final: 0.7054 (t0) REVERT: B 100 MET cc_start: 0.5688 (tpt) cc_final: 0.5266 (tpt) REVERT: B 264 ARG cc_start: 0.6394 (mtm110) cc_final: 0.5967 (mtm110) REVERT: B 313 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7099 (mp) REVERT: B 325 GLN cc_start: 0.3324 (OUTLIER) cc_final: 0.2878 (tm-30) outliers start: 28 outliers final: 21 residues processed: 150 average time/residue: 0.1109 time to fit residues: 21.3700 Evaluate side-chains 160 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 364 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** 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 = 0.4425 r_free = 0.4425 target = 0.204738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.166716 restraints weight = 12435.183| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.19 r_work: 0.3796 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8573 Z= 0.167 Angle : 0.608 10.808 12027 Z= 0.329 Chirality : 0.040 0.213 1384 Planarity : 0.005 0.053 1106 Dihedral : 20.395 162.791 2339 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.97 % Favored : 95.89 % Rotamer: Outliers : 4.10 % Allowed : 29.81 % Favored : 66.09 % 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: -0.23 (0.31), residues: 705 helix: 1.15 (0.27), residues: 345 sheet: -1.39 (0.46), residues: 123 loop : -1.31 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 184 TYR 0.017 0.001 TYR B 60 PHE 0.020 0.002 PHE A 139 TRP 0.023 0.002 TRP B 34 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 8573) covalent geometry : angle 0.60777 / 0.33 (12027) hydrogen bonds : bond 0.04710 / 3.10 ( 430) hydrogen bonds : angle 4.33794 / 3.10 ( 1153) ********************** 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 161 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7778 (mtt-85) REVERT: A 196 ASN cc_start: 0.7692 (m-40) cc_final: 0.7403 (m-40) REVERT: A 248 THR cc_start: 0.7145 (OUTLIER) cc_final: 0.6744 (m) REVERT: A 259 ILE cc_start: 0.7502 (mt) cc_final: 0.7176 (tt) REVERT: A 266 THR cc_start: 0.7543 (m) cc_final: 0.7319 (p) REVERT: A 277 LYS cc_start: 0.7954 (tptt) cc_final: 0.7478 (mmmm) REVERT: A 280 LYS cc_start: 0.5699 (mttm) cc_final: 0.5264 (mttm) REVERT: B 57 ASP cc_start: 0.7371 (t0) cc_final: 0.7169 (t0) REVERT: B 100 MET cc_start: 0.5686 (tpt) cc_final: 0.5277 (tpt) REVERT: B 119 ASN cc_start: 0.6718 (m110) cc_final: 0.6286 (m110) REVERT: B 168 LYS cc_start: 0.6883 (pttt) cc_final: 0.6427 (mtmt) REVERT: B 203 LYS cc_start: 0.6081 (mttt) cc_final: 0.5706 (mttt) REVERT: B 264 ARG cc_start: 0.6366 (mtm110) cc_final: 0.5972 (mtm110) REVERT: B 313 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7031 (mp) REVERT: B 325 GLN cc_start: 0.3349 (OUTLIER) cc_final: 0.2908 (tm-30) outliers start: 26 outliers final: 19 residues processed: 147 average time/residue: 0.1062 time to fit residues: 19.8692 Evaluate side-chains 156 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 325 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** 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 = 0.4405 r_free = 0.4405 target = 0.202866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.164811 restraints weight = 12520.143| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.20 r_work: 0.3755 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.6062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8573 Z= 0.213 Angle : 0.641 9.608 12027 Z= 0.351 Chirality : 0.042 0.217 1384 Planarity : 0.005 0.060 1106 Dihedral : 20.446 163.720 2337 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.83 % Favored : 96.03 % Rotamer: Outliers : 3.94 % Allowed : 30.60 % Favored : 65.46 % 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: -0.38 (0.31), residues: 705 helix: 0.95 (0.27), residues: 345 sheet: -1.36 (0.46), residues: 123 loop : -1.32 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 256 TYR 0.017 0.002 TYR B 60 PHE 0.021 0.002 PHE A 139 TRP 0.027 0.003 TRP B 34 HIS 0.006 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 ( 8573) covalent geometry : angle 0.64118 / 0.35 (12027) hydrogen bonds : bond 0.05095 / 3.34 ( 430) hydrogen bonds : angle 4.46421 / 3.19 ( 1153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1749.18 seconds wall clock time: 30 minutes 39.94 seconds (1839.94 seconds total)