Starting phenix.real_space_refine on Thu Jul 2 10:09:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9o_49174/07_2026/9n9o_49174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9o_49174/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9n9o_49174/07_2026/9n9o_49174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9o_49174/07_2026/9n9o_49174.map" model { file = "/net/cci-nas-00/data/ceres_data/9n9o_49174/07_2026/9n9o_49174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9o_49174/07_2026/9n9o_49174_neut.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.36, per 1000 atoms: 0.17 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: 0.47 Conformation dependent library (CDL) restraints added in 254.9 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: 0.94 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: 1.07 Time building geometry restraints manager: 0.68 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: 11756 2.03 - 4.06: 237 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=" N3 DT b -10 " pdb=" C4 DT b -10 " pdb=" O4 DT b -10 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT b -8 " pdb=" C4 DT b -8 " pdb=" O4 DT b -8 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+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: 987 0.040 - 0.080: 281 0.080 - 0.120: 97 0.120 - 0.160: 17 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: 1.030 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.700 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.990 ------------------------------------------------------------------------------- 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= 0.390 Angle : 0.706 10.139 12027 Z= 0.499 Chirality : 0.043 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 0.00523 / 0.39 ( 8573) covalent geometry : angle 0.70575 / 0.50 (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 : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.5703 (mm-30) cc_final: 0.5392 (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: 0.5952 (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: 0.6353 (ttt) REVERT: B 57 ASP cc_start: 0.7232 (t0) cc_final: 0.6841 (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: 0.7967 (mttt) outliers start: 21 outliers final: 6 residues processed: 150 average time/residue: 0.0931 time to fit residues: 18.2837 Evaluate side-chains 129 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 299 HIS B 242 ASN B 299 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.211764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.174380 restraints weight = 12894.530| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.38 r_work: 0.3916 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 8573 Z= 0.348 Angle : 0.790 9.629 12027 Z= 0.442 Chirality : 0.050 0.267 1384 Planarity : 0.006 0.064 1106 Dihedral : 20.465 167.266 2352 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.69 % Favored : 96.17 % Rotamer: Outliers : 5.52 % Allowed : 27.92 % Favored : 66.56 % 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: -0.72 (0.30), residues: 705 helix: 0.39 (0.25), residues: 344 sheet: -0.77 (0.48), residues: 124 loop : -1.47 (0.39), residues: 237 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 0.019 0.003 TRP B 34 HIS 0.011 0.002 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.35 ( 8573) covalent geometry : angle 0.78955 / 0.44 (12027) hydrogen bonds : bond 0.06468 / 4.36 ( 430) hydrogen bonds : angle 4.87331 / 3.54 ( 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 172 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.7518 (mt) cc_final: 0.7215 (mt) REVERT: A 65 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7610 (pt) REVERT: A 180 MET cc_start: 0.7115 (ttp) cc_final: 0.6779 (ttp) REVERT: A 196 ASN cc_start: 0.7420 (m-40) cc_final: 0.7117 (m-40) REVERT: A 248 THR cc_start: 0.6345 (OUTLIER) cc_final: 0.5712 (m) REVERT: A 277 LYS cc_start: 0.7141 (tptt) cc_final: 0.6808 (tptt) REVERT: A 302 HIS cc_start: 0.6999 (OUTLIER) cc_final: 0.5342 (m-70) REVERT: A 303 VAL cc_start: 0.7425 (m) cc_final: 0.7192 (t) REVERT: A 323 MET cc_start: 0.6776 (mmm) cc_final: 0.6553 (mmm) REVERT: B 10 ARG cc_start: 0.7386 (mmt-90) cc_final: 0.6993 (mmt-90) REVERT: B 57 ASP cc_start: 0.7694 (t0) cc_final: 0.7191 (t0) REVERT: B 125 LYS cc_start: 0.7868 (mttt) cc_final: 0.7562 (mttt) REVERT: B 168 LYS cc_start: 0.7048 (pttt) cc_final: 0.6743 (pttt) REVERT: B 187 LYS cc_start: 0.8277 (mttt) cc_final: 0.7893 (mttt) REVERT: B 232 GLU cc_start: 0.4937 (pp20) cc_final: 0.4611 (pp20) REVERT: B 295 ASN cc_start: 0.6982 (t0) cc_final: 0.6504 (t0) REVERT: B 313 ILE cc_start: 0.7205 (mp) cc_final: 0.6967 (mp) REVERT: B 325 GLN cc_start: 0.3701 (OUTLIER) cc_final: 0.3211 (tm-30) REVERT: B 339 LEU cc_start: 0.3007 (mm) cc_final: 0.2625 (mt) outliers start: 35 outliers final: 15 residues processed: 166 average time/residue: 0.1020 time to fit residues: 22.2414 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 : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 186 VAL 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 A residue 305 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 LEU 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: 4.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 overall best weight: 1.2388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.212053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.174650 restraints weight = 12615.840| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.28 r_work: 0.3913 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8573 Z= 0.206 Angle : 0.607 7.605 12027 Z= 0.349 Chirality : 0.041 0.161 1384 Planarity : 0.005 0.057 1106 Dihedral : 20.357 165.591 2343 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 5.05 % Allowed : 27.13 % Favored : 67.82 % 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 (0.32), residues: 705 helix: 0.98 (0.27), residues: 343 sheet: -0.86 (0.48), residues: 123 loop : -1.34 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 40 TYR 0.023 0.002 TYR B 254 PHE 0.021 0.002 PHE A 39 TRP 0.013 0.001 TRP B 34 HIS 0.005 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.21 ( 8573) covalent geometry : angle 0.60676 / 0.35 (12027) hydrogen bonds : bond 0.05070 / 3.39 ( 430) hydrogen bonds : angle 4.55916 / 3.30 ( 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 165 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7782 (mmt180) REVERT: A 45 ILE cc_start: 0.7773 (mm) cc_final: 0.7545 (mt) REVERT: A 65 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7653 (pt) REVERT: A 183 GLU cc_start: 0.7239 (pt0) cc_final: 0.6985 (pt0) REVERT: A 196 ASN cc_start: 0.7522 (m-40) cc_final: 0.7191 (m-40) REVERT: A 248 THR cc_start: 0.6392 (OUTLIER) cc_final: 0.5931 (m) REVERT: A 266 THR cc_start: 0.7429 (m) cc_final: 0.7142 (p) REVERT: A 274 ARG cc_start: 0.7557 (tpt170) cc_final: 0.6949 (tpt170) REVERT: A 277 LYS cc_start: 0.7401 (tptt) cc_final: 0.7171 (tptt) REVERT: A 302 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.4423 (m170) REVERT: A 303 VAL cc_start: 0.7492 (m) cc_final: 0.7239 (t) REVERT: A 323 MET cc_start: 0.6655 (mmm) cc_final: 0.6389 (mmm) REVERT: B 15 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5655 (tt) REVERT: B 25 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7452 (mmmm) REVERT: B 54 MET cc_start: 0.6753 (mmm) cc_final: 0.6291 (mmt) REVERT: B 57 ASP cc_start: 0.7723 (t0) cc_final: 0.7380 (t0) REVERT: B 100 MET cc_start: 0.5699 (tpt) cc_final: 0.5286 (tpt) REVERT: B 125 LYS cc_start: 0.7825 (mttt) cc_final: 0.7563 (mttt) REVERT: B 168 LYS cc_start: 0.6889 (pttt) cc_final: 0.6441 (mtmm) REVERT: B 187 LYS cc_start: 0.8212 (mttt) cc_final: 0.7822 (mttt) REVERT: B 295 ASN cc_start: 0.7169 (t0) cc_final: 0.6819 (t0) REVERT: B 313 ILE cc_start: 0.7221 (mp) cc_final: 0.6983 (mp) REVERT: B 325 GLN cc_start: 0.3608 (OUTLIER) cc_final: 0.3146 (tm-30) REVERT: B 339 LEU cc_start: 0.3150 (mm) cc_final: 0.2700 (mt) REVERT: B 346 GLU cc_start: 0.7281 (mp0) cc_final: 0.7074 (mp0) outliers start: 32 outliers final: 15 residues processed: 157 average time/residue: 0.0996 time to fit residues: 20.1217 Evaluate side-chains 152 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 106 SER 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 302 HIS 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 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: 0.9980 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** 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 B 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.211100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.177788 restraints weight = 12941.995| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.30 r_work: 0.3871 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.3692 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= 0.170 Angle : 0.570 8.411 12027 Z= 0.325 Chirality : 0.039 0.156 1384 Planarity : 0.004 0.049 1106 Dihedral : 20.347 164.126 2343 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.60 % Rotamer: Outliers : 5.21 % Allowed : 25.87 % 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: -0.21 (0.32), residues: 705 helix: 1.04 (0.27), residues: 343 sheet: -1.02 (0.48), residues: 123 loop : -1.30 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 263 TYR 0.017 0.002 TYR B 60 PHE 0.021 0.002 PHE B 116 TRP 0.010 0.001 TRP B 34 HIS 0.007 0.002 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 ( 8573) covalent geometry : angle 0.56970 / 0.32 (12027) hydrogen bonds : bond 0.04654 / 3.14 ( 430) hydrogen bonds : angle 4.47306 / 3.22 ( 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 167 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8069 (mmm-85) REVERT: A 54 MET cc_start: 0.7115 (mmm) cc_final: 0.6755 (ttm) REVERT: A 65 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7726 (pt) REVERT: A 183 GLU cc_start: 0.7289 (pt0) cc_final: 0.7073 (pt0) REVERT: A 196 ASN cc_start: 0.7566 (m-40) cc_final: 0.7232 (m-40) REVERT: A 248 THR cc_start: 0.6493 (OUTLIER) cc_final: 0.6014 (m) REVERT: A 266 THR cc_start: 0.7495 (m) cc_final: 0.7242 (p) REVERT: A 277 LYS cc_start: 0.7504 (tptt) cc_final: 0.7055 (tppp) REVERT: A 302 HIS cc_start: 0.7147 (OUTLIER) cc_final: 0.4323 (m170) REVERT: A 303 VAL cc_start: 0.7583 (m) cc_final: 0.7320 (t) REVERT: A 323 MET cc_start: 0.6647 (mmm) cc_final: 0.6389 (mmm) REVERT: B 15 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5681 (tt) REVERT: B 25 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7417 (mmmm) REVERT: B 54 MET cc_start: 0.6823 (mmm) cc_final: 0.6414 (mmt) REVERT: B 57 ASP cc_start: 0.7811 (t0) cc_final: 0.7440 (t0) REVERT: B 125 LYS cc_start: 0.7867 (mttt) cc_final: 0.7645 (mttt) REVERT: B 168 LYS cc_start: 0.6841 (pttt) cc_final: 0.6358 (mtmm) REVERT: B 187 LYS cc_start: 0.8186 (mttt) cc_final: 0.7745 (mttt) REVERT: B 264 ARG cc_start: 0.6294 (mtm110) cc_final: 0.5997 (mtm110) REVERT: B 295 ASN cc_start: 0.7471 (t0) cc_final: 0.7176 (t0) REVERT: B 313 ILE cc_start: 0.7181 (mp) cc_final: 0.6918 (mp) REVERT: B 325 GLN cc_start: 0.3624 (OUTLIER) cc_final: 0.2426 (tm-30) REVERT: B 326 GLU cc_start: 0.3190 (OUTLIER) cc_final: 0.2418 (tt0) REVERT: B 339 LEU cc_start: 0.3417 (mm) cc_final: 0.2865 (mt) outliers start: 33 outliers final: 17 residues processed: 158 average time/residue: 0.0928 time to fit residues: 19.1039 Evaluate side-chains 156 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 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 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 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 268 VAL 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 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 326 GLU 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: 10.0000 chunk 67 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** 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 = 0.4478 r_free = 0.4478 target = 0.209640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.173525 restraints weight = 12769.909| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.31 r_work: 0.3860 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8573 Z= 0.174 Angle : 0.563 7.495 12027 Z= 0.321 Chirality : 0.039 0.174 1384 Planarity : 0.004 0.045 1106 Dihedral : 20.370 163.841 2343 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer: Outliers : 6.31 % Allowed : 25.87 % Favored : 67.82 % 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: -0.15 (0.32), residues: 705 helix: 1.12 (0.27), residues: 344 sheet: -1.12 (0.47), residues: 123 loop : -1.24 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 263 TYR 0.017 0.002 TYR B 60 PHE 0.019 0.002 PHE B 116 TRP 0.014 0.002 TRP B 342 HIS 0.009 0.002 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 ( 8573) covalent geometry : angle 0.56309 / 0.32 (12027) hydrogen bonds : bond 0.04587 / 3.04 ( 430) hydrogen bonds : angle 4.36783 / 3.15 ( 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 170 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7940 (mmm-85) REVERT: A 28 MET cc_start: 0.7586 (mmm) cc_final: 0.7150 (mmt) REVERT: A 65 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7830 (pt) REVERT: A 196 ASN cc_start: 0.7586 (m-40) cc_final: 0.7264 (m-40) REVERT: A 211 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6515 (mm-30) REVERT: A 248 THR cc_start: 0.6629 (OUTLIER) cc_final: 0.6154 (m) REVERT: A 250 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6555 (tm-30) REVERT: A 266 THR cc_start: 0.7495 (m) cc_final: 0.7250 (p) REVERT: A 277 LYS cc_start: 0.7701 (tptt) cc_final: 0.7154 (mmmm) REVERT: A 302 HIS cc_start: 0.7136 (OUTLIER) cc_final: 0.5708 (m-70) REVERT: A 303 VAL cc_start: 0.7522 (m) cc_final: 0.7288 (t) REVERT: B 15 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5683 (tt) REVERT: B 25 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7408 (mmmm) REVERT: B 54 MET cc_start: 0.6770 (mmm) cc_final: 0.6442 (mmt) REVERT: B 57 ASP cc_start: 0.7794 (t0) cc_final: 0.7394 (t0) REVERT: B 100 MET cc_start: 0.5745 (tpt) cc_final: 0.5405 (tpt) REVERT: B 125 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7605 (mttt) REVERT: B 168 LYS cc_start: 0.6897 (pttt) cc_final: 0.6391 (mtmm) REVERT: B 264 ARG cc_start: 0.6394 (mtm110) cc_final: 0.6050 (mtm110) REVERT: B 295 ASN cc_start: 0.7555 (t0) cc_final: 0.7320 (t0) REVERT: B 313 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.6985 (mp) REVERT: B 325 GLN cc_start: 0.2876 (OUTLIER) cc_final: 0.2486 (tm-30) REVERT: B 339 LEU cc_start: 0.3472 (mm) cc_final: 0.2992 (mt) REVERT: B 346 GLU cc_start: 0.7119 (mp0) cc_final: 0.6758 (mp0) outliers start: 40 outliers final: 20 residues processed: 154 average time/residue: 0.0972 time to fit residues: 19.3263 Evaluate side-chains 157 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 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 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 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 125 LYS Chi-restraints excluded: chain B residue 143 LEU 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 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: 0.6980 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.209981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.173591 restraints weight = 12604.330| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.33 r_work: 0.3860 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8573 Z= 0.141 Angle : 0.528 9.665 12027 Z= 0.301 Chirality : 0.038 0.158 1384 Planarity : 0.004 0.047 1106 Dihedral : 20.354 162.710 2343 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.40 % Favored : 96.45 % Rotamer: Outliers : 5.36 % Allowed : 28.86 % Favored : 65.77 % 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: -0.17 (0.32), residues: 705 helix: 1.12 (0.27), residues: 345 sheet: -1.25 (0.46), residues: 123 loop : -1.22 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 40 TYR 0.017 0.001 TYR B 60 PHE 0.017 0.002 PHE A 39 TRP 0.013 0.001 TRP B 34 HIS 0.007 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 8573) covalent geometry : angle 0.52793 / 0.30 (12027) hydrogen bonds : bond 0.04363 / 2.88 ( 430) hydrogen bonds : angle 4.33721 / 3.11 ( 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 164 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.7772 (mmm) cc_final: 0.7458 (mmt) REVERT: A 54 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6813 (ttm) REVERT: A 196 ASN cc_start: 0.7585 (m-40) cc_final: 0.7265 (m-40) REVERT: A 211 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6538 (mm-30) REVERT: A 248 THR cc_start: 0.6658 (OUTLIER) cc_final: 0.6211 (m) REVERT: A 250 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6553 (tm-30) REVERT: A 266 THR cc_start: 0.7500 (m) cc_final: 0.7248 (p) REVERT: A 302 HIS cc_start: 0.7139 (OUTLIER) cc_final: 0.5733 (m-70) REVERT: A 303 VAL cc_start: 0.7532 (m) cc_final: 0.7260 (t) REVERT: B 15 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5702 (tt) REVERT: B 25 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7436 (mmmm) REVERT: B 54 MET cc_start: 0.6739 (mmm) cc_final: 0.6429 (mmt) REVERT: B 57 ASP cc_start: 0.7860 (t0) cc_final: 0.7478 (t0) REVERT: B 100 MET cc_start: 0.5675 (tpt) cc_final: 0.5211 (tpt) REVERT: B 125 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7623 (mttt) REVERT: B 168 LYS cc_start: 0.6922 (pttt) cc_final: 0.6434 (mtmm) REVERT: B 264 ARG cc_start: 0.6323 (mtm110) cc_final: 0.6025 (mtm110) REVERT: B 313 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6994 (mp) REVERT: B 323 MET cc_start: 0.6696 (mmm) cc_final: 0.6438 (mmm) REVERT: B 325 GLN cc_start: 0.2829 (OUTLIER) cc_final: 0.2461 (tm-30) REVERT: B 339 LEU cc_start: 0.3589 (mm) cc_final: 0.3046 (mt) REVERT: B 346 GLU cc_start: 0.6961 (mp0) cc_final: 0.5770 (mp0) outliers start: 34 outliers final: 18 residues processed: 151 average time/residue: 0.0920 time to fit residues: 17.9314 Evaluate side-chains 150 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE 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 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 25 LYS Chi-restraints excluded: chain B residue 47 THR 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 143 LEU 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 364 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 61 optimal weight: 50.0000 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 HIS B 316 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.204199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.165764 restraints weight = 12781.348| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.30 r_work: 0.3787 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8573 Z= 0.286 Angle : 0.692 8.838 12027 Z= 0.385 Chirality : 0.046 0.184 1384 Planarity : 0.006 0.070 1106 Dihedral : 20.425 166.222 2343 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.68 % Favored : 95.18 % Rotamer: Outliers : 6.62 % Allowed : 27.60 % Favored : 65.77 % 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: -0.67 (0.31), residues: 705 helix: 0.56 (0.27), residues: 343 sheet: -1.38 (0.46), residues: 123 loop : -1.25 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 184 TYR 0.046 0.003 TYR B 345 PHE 0.024 0.002 PHE A 39 TRP 0.013 0.003 TRP A 342 HIS 0.009 0.002 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.29 ( 8573) covalent geometry : angle 0.69239 / 0.39 (12027) hydrogen bonds : bond 0.05717 / 3.75 ( 430) hydrogen bonds : angle 4.59225 / 3.30 ( 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 176 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8071 (mmm-85) REVERT: A 28 MET cc_start: 0.8012 (mmm) cc_final: 0.7679 (tpp) REVERT: A 30 MET cc_start: 0.7043 (ttm) cc_final: 0.6823 (ttt) REVERT: A 56 LYS cc_start: 0.7982 (ttpp) cc_final: 0.7636 (ttpp) REVERT: A 68 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7377 (mmmt) REVERT: A 124 TRP cc_start: 0.7089 (OUTLIER) cc_final: 0.6701 (m100) REVERT: A 211 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6336 (mm-30) REVERT: A 266 THR cc_start: 0.7522 (m) cc_final: 0.7296 (p) REVERT: A 277 LYS cc_start: 0.7944 (tptt) cc_final: 0.7356 (mmmm) REVERT: A 280 LYS cc_start: 0.5523 (mttp) cc_final: 0.5103 (mttp) REVERT: B 100 MET cc_start: 0.5877 (tpt) cc_final: 0.5434 (tpt) REVERT: B 119 ASN cc_start: 0.6887 (m110) cc_final: 0.6409 (m-40) REVERT: B 125 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7739 (mttt) REVERT: B 168 LYS cc_start: 0.6982 (pttt) cc_final: 0.6506 (mtmm) REVERT: B 184 ARG cc_start: 0.8438 (mtm110) cc_final: 0.8209 (ptp90) REVERT: B 187 LYS cc_start: 0.8198 (mttt) cc_final: 0.7751 (mttt) REVERT: B 220 LYS cc_start: 0.7647 (mttt) cc_final: 0.7334 (mttt) REVERT: B 264 ARG cc_start: 0.6343 (mtm110) cc_final: 0.5823 (mtm110) REVERT: B 313 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7105 (mp) REVERT: B 325 GLN cc_start: 0.3338 (OUTLIER) cc_final: 0.2919 (tm-30) REVERT: B 346 GLU cc_start: 0.7292 (mp0) cc_final: 0.7011 (mp0) outliers start: 42 outliers final: 26 residues processed: 162 average time/residue: 0.1091 time to fit residues: 22.5191 Evaluate side-chains 162 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 150 VAL 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 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 12 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 124 TRP Chi-restraints excluded: chain B residue 125 LYS 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 245 THR Chi-restraints excluded: chain B residue 251 GLU 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 344 TYR 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: 50.0000 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 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 = 0.4451 r_free = 0.4451 target = 0.206744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.172311 restraints weight = 12641.803| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.27 r_work: 0.3820 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8573 Z= 0.156 Angle : 0.573 11.400 12027 Z= 0.319 Chirality : 0.039 0.155 1384 Planarity : 0.004 0.048 1106 Dihedral : 20.432 163.711 2343 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.88 % Rotamer: Outliers : 4.89 % Allowed : 29.50 % 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: -0.39 (0.31), residues: 705 helix: 0.92 (0.27), residues: 344 sheet: -1.40 (0.46), residues: 123 loop : -1.24 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 40 TYR 0.016 0.002 TYR B 60 PHE 0.023 0.002 PHE A 139 TRP 0.011 0.002 TRP B 34 HIS 0.009 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 ( 8573) covalent geometry : angle 0.57289 / 0.32 (12027) hydrogen bonds : bond 0.04572 / 3.02 ( 430) hydrogen bonds : angle 4.37854 / 3.13 ( 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 163 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8097 (mmm-85) REVERT: A 28 MET cc_start: 0.7877 (mmm) cc_final: 0.7540 (mmt) REVERT: A 30 MET cc_start: 0.6811 (ttm) cc_final: 0.6606 (ttt) REVERT: A 211 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6401 (mm-30) REVERT: A 248 THR cc_start: 0.6971 (OUTLIER) cc_final: 0.6516 (m) REVERT: A 251 GLU cc_start: 0.6741 (tt0) cc_final: 0.6521 (tt0) REVERT: A 259 ILE cc_start: 0.7015 (mt) cc_final: 0.6739 (tt) REVERT: A 266 THR cc_start: 0.7588 (m) cc_final: 0.7349 (p) REVERT: A 277 LYS cc_start: 0.7900 (tptt) cc_final: 0.7376 (mmmm) REVERT: A 280 LYS cc_start: 0.5593 (mttp) cc_final: 0.5171 (mttp) REVERT: B 100 MET cc_start: 0.5845 (tpt) cc_final: 0.5455 (tpt) REVERT: B 168 LYS cc_start: 0.6942 (pttt) cc_final: 0.6501 (mtmt) REVERT: B 264 ARG cc_start: 0.6291 (mtm110) cc_final: 0.5859 (mtm110) REVERT: B 313 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.7016 (mp) REVERT: B 325 GLN cc_start: 0.3324 (OUTLIER) cc_final: 0.2886 (tm-30) REVERT: B 339 LEU cc_start: 0.4304 (mm) cc_final: 0.3797 (mt) REVERT: B 346 GLU cc_start: 0.7130 (mp0) cc_final: 0.6812 (mp0) outliers start: 31 outliers final: 22 residues processed: 151 average time/residue: 0.1027 time to fit residues: 19.8727 Evaluate side-chains 158 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain A residue 62 SER 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 190 VAL 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 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 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 338 VAL 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: 4.9990 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.205354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.170382 restraints weight = 12573.193| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.30 r_work: 0.3775 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.5309 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= 0.176 Angle : 0.587 10.691 12027 Z= 0.326 Chirality : 0.040 0.172 1384 Planarity : 0.004 0.048 1106 Dihedral : 20.401 164.454 2343 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.11 % Favored : 95.74 % Rotamer: Outliers : 4.73 % Allowed : 30.13 % Favored : 65.14 % 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: -0.32 (0.31), residues: 705 helix: 0.99 (0.27), residues: 344 sheet: -1.41 (0.45), residues: 123 loop : -1.20 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 184 TYR 0.019 0.002 TYR B 345 PHE 0.018 0.002 PHE A 139 TRP 0.017 0.002 TRP B 34 HIS 0.005 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 ( 8573) covalent geometry : angle 0.58714 / 0.33 (12027) hydrogen bonds : bond 0.04785 / 3.15 ( 430) hydrogen bonds : angle 4.36655 / 3.12 ( 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 158 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8090 (mmm-85) REVERT: A 28 MET cc_start: 0.7912 (mmm) cc_final: 0.7613 (tpp) REVERT: A 30 MET cc_start: 0.6993 (ttm) cc_final: 0.6787 (ttt) REVERT: A 40 ARG cc_start: 0.8121 (mtt-85) cc_final: 0.7856 (mtt-85) REVERT: A 211 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6408 (mm-30) REVERT: A 248 THR cc_start: 0.7099 (OUTLIER) cc_final: 0.6669 (m) REVERT: A 266 THR cc_start: 0.7615 (m) cc_final: 0.7384 (p) REVERT: A 280 LYS cc_start: 0.5842 (mttp) cc_final: 0.5423 (mttp) REVERT: B 10 ARG cc_start: 0.7263 (mmt-90) cc_final: 0.7017 (mmt180) REVERT: B 100 MET cc_start: 0.5761 (tpt) cc_final: 0.5310 (tpt) REVERT: B 119 ASN cc_start: 0.6746 (m110) cc_final: 0.6304 (m110) REVERT: B 256 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7732 (mmm-85) REVERT: B 264 ARG cc_start: 0.6391 (mtm110) cc_final: 0.5881 (mtm110) REVERT: B 325 GLN cc_start: 0.3351 (OUTLIER) cc_final: 0.2907 (tm-30) REVERT: B 346 GLU cc_start: 0.7090 (mp0) cc_final: 0.6792 (mp0) outliers start: 30 outliers final: 22 residues processed: 144 average time/residue: 0.1013 time to fit residues: 18.5247 Evaluate side-chains 151 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 62 SER 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 190 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 248 THR 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 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 248 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 344 TYR 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: 0.8980 chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.202150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.163842 restraints weight = 12411.947| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.22 r_work: 0.3768 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 8573 Z= 0.262 Angle : 0.691 10.571 12027 Z= 0.381 Chirality : 0.044 0.172 1384 Planarity : 0.006 0.072 1106 Dihedral : 20.563 166.830 2341 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.82 % Favored : 95.04 % Rotamer: Outliers : 4.42 % Allowed : 30.13 % 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: -0.64 (0.31), residues: 705 helix: 0.66 (0.27), residues: 344 sheet: -1.50 (0.45), residues: 123 loop : -1.29 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 256 TYR 0.025 0.002 TYR A 296 PHE 0.023 0.002 PHE A 39 TRP 0.028 0.004 TRP A 342 HIS 0.007 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.26 ( 8573) covalent geometry : angle 0.69078 / 0.38 (12027) hydrogen bonds : bond 0.05565 / 3.65 ( 430) hydrogen bonds : angle 4.63532 / 3.31 ( 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 162 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8044 (mmm-85) REVERT: A 28 MET cc_start: 0.8021 (mmm) cc_final: 0.7728 (tpp) REVERT: A 248 THR cc_start: 0.7297 (OUTLIER) cc_final: 0.6888 (m) REVERT: A 266 THR cc_start: 0.7574 (m) cc_final: 0.7360 (p) REVERT: A 277 LYS cc_start: 0.8254 (mptt) cc_final: 0.7737 (mmmm) REVERT: A 280 LYS cc_start: 0.6073 (mttp) cc_final: 0.5651 (mttp) REVERT: B 100 MET cc_start: 0.5799 (tpt) cc_final: 0.5403 (tpt) REVERT: B 203 LYS cc_start: 0.6088 (mttt) cc_final: 0.5730 (mttt) REVERT: B 220 LYS cc_start: 0.7665 (mttt) cc_final: 0.7342 (mttt) REVERT: B 256 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7739 (mmm-85) REVERT: B 264 ARG cc_start: 0.6276 (mtm110) cc_final: 0.5869 (mtm110) REVERT: B 313 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.7120 (mp) REVERT: B 325 GLN cc_start: 0.3389 (OUTLIER) cc_final: 0.2947 (tm-30) REVERT: B 346 GLU cc_start: 0.6938 (mp0) cc_final: 0.6599 (mp0) outliers start: 28 outliers final: 17 residues processed: 147 average time/residue: 0.1051 time to fit residues: 19.7588 Evaluate side-chains 153 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 62 SER 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 190 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.0040 chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 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 = 0.4413 r_free = 0.4413 target = 0.203417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.165324 restraints weight = 12608.402| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.22 r_work: 0.3773 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8573 Z= 0.186 Angle : 0.626 11.442 12027 Z= 0.342 Chirality : 0.041 0.148 1384 Planarity : 0.005 0.051 1106 Dihedral : 20.532 165.788 2339 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.11 % Favored : 95.74 % Rotamer: Outliers : 3.15 % Allowed : 32.33 % Favored : 64.51 % 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: -0.47 (0.31), residues: 705 helix: 0.88 (0.27), residues: 344 sheet: -1.48 (0.46), residues: 123 loop : -1.30 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 40 TYR 0.020 0.002 TYR B 345 PHE 0.022 0.002 PHE A 139 TRP 0.020 0.003 TRP A 342 HIS 0.004 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 ( 8573) covalent geometry : angle 0.62611 / 0.34 (12027) hydrogen bonds : bond 0.04888 / 3.24 ( 430) hydrogen bonds : angle 4.47518 / 3.20 ( 1153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1700.67 seconds wall clock time: 29 minutes 51.02 seconds (1791.02 seconds total)