Starting phenix.real_space_refine on Fri Sep 11 03:20:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qnu_4609/09_2026/6qnu_4609.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qnu_4609/09_2026/6qnu_4609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qnu_4609/09_2026/6qnu_4609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qnu_4609/09_2026/6qnu_4609.map" model { file = "/net/cci-nas-00/data/ceres_data/6qnu_4609/09_2026/6qnu_4609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qnu_4609/09_2026/6qnu_4609.cif" } resolution = 3.8 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= -0.000 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4655 2.51 5 N 1169 2.21 5 O 1404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7250 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1400 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 2 Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1424 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 11, 'TRANS': 169} Chain breaks: 2 Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1409 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 2 Chain: "D" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1541 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Chain: "E" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain breaks: 5 Time building chain proxies: 1.48, per 1000 atoms: 0.20 Number of scatterers: 7250 At special positions: 0 Unit cell: (94.963, 105.633, 93.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1404 8.00 N 1169 7.00 C 4655 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: 0.46 Conformation dependent library (CDL) restraints added in 259.4 milliseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1742 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 17 sheets defined 2.8% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.583A pdb=" N ASN B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.153A pdb=" N PHE C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 270 removed outlier: 4.424A pdb=" N GLY E 269 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 197 removed outlier: 3.508A pdb=" N VAL A 269 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA4, first strand: chain 'B' and resid 188 through 196 removed outlier: 3.734A pdb=" N LEU B 289 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASN B 293 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 132 through 133 removed outlier: 4.175A pdb=" N LEU C 305 " --> pdb=" O GLY C 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 132 through 133 removed outlier: 3.652A pdb=" N PHE C 312 " --> pdb=" O GLY C 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 197 removed outlier: 5.542A pdb=" N ASN C 293 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.401A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 191 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 151 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG D 193 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR D 149 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.854A pdb=" N ILE D 171 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 170 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 222 through 223 removed outlier: 3.722A pdb=" N VAL D 222 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLU D 240 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU D 287 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR D 242 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 259 through 263 removed outlier: 3.753A pdb=" N VAL D 303 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 324 " --> pdb=" O VAL D 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 114 through 120 removed outlier: 6.511A pdb=" N PHE E 115 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ARG E 212 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY E 117 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU E 214 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL E 119 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 190 " --> pdb=" O ALA E 207 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR E 187 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU E 154 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR E 189 " --> pdb=" O VAL E 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.724A pdb=" N ILE E 171 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 222 through 223 removed outlier: 3.521A pdb=" N VAL E 222 " --> pdb=" O PHE E 247 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 229 through 232 removed outlier: 6.681A pdb=" N GLY E 230 " --> pdb=" O LYS E 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 259 through 261 Processing sheet with id=AB8, first strand: chain 'E' and resid 272 through 277 188 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2260 1.34 - 1.46: 1349 1.46 - 1.57: 3752 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 7399 Sorted by residual: bond pdb=" C GLU E 155 " pdb=" N PRO E 156 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.68e+00 bond pdb=" C GLU D 155 " pdb=" N PRO D 156 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.44e+00 bond pdb=" CA THR A 304 " pdb=" CB THR A 304 " ideal model delta sigma weight residual 1.530 1.559 -0.029 1.69e-02 3.50e+03 2.95e+00 bond pdb=" CA TYR D 158 " pdb=" C TYR D 158 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.64e+00 bond pdb=" CA TYR E 158 " pdb=" C TYR E 158 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.63e+00 ... (remaining 7394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 9719 2.17 - 4.34: 270 4.34 - 6.51: 39 6.51 - 8.68: 18 8.68 - 10.85: 4 Bond angle restraints: 10050 Sorted by residual: angle pdb=" C ALA A 303 " pdb=" N THR A 304 " pdb=" CA THR A 304 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C ASN D 219 " pdb=" N ILE D 220 " pdb=" CA ILE D 220 " ideal model delta sigma weight residual 122.13 130.06 -7.93 1.85e+00 2.92e-01 1.84e+01 angle pdb=" N ILE D 315 " pdb=" CA ILE D 315 " pdb=" C ILE D 315 " ideal model delta sigma weight residual 113.71 109.68 4.03 9.50e-01 1.11e+00 1.80e+01 angle pdb=" C ASP D 218 " pdb=" N ASN D 219 " pdb=" CA ASN D 219 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 angle pdb=" N TRP D 257 " pdb=" CA TRP D 257 " pdb=" C TRP D 257 " ideal model delta sigma weight residual 114.04 109.06 4.98 1.24e+00 6.50e-01 1.62e+01 ... (remaining 10045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 3940 16.84 - 33.69: 390 33.69 - 50.53: 66 50.53 - 67.37: 11 67.37 - 84.22: 6 Dihedral angle restraints: 4413 sinusoidal: 1724 harmonic: 2689 Sorted by residual: dihedral pdb=" CA LEU A 273 " pdb=" C LEU A 273 " pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta harmonic sigma weight residual -180.00 -138.37 -41.63 0 5.00e+00 4.00e-02 6.93e+01 dihedral pdb=" CA LEU B 273 " pdb=" C LEU B 273 " pdb=" N ASN B 274 " pdb=" CA ASN B 274 " ideal model delta harmonic sigma weight residual -180.00 -145.15 -34.85 0 5.00e+00 4.00e-02 4.86e+01 dihedral pdb=" CA ASP D 218 " pdb=" C ASP D 218 " pdb=" N ASN D 219 " pdb=" CA ASN D 219 " ideal model delta harmonic sigma weight residual -180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 ... (remaining 4410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 845 0.053 - 0.106: 236 0.106 - 0.159: 77 0.159 - 0.211: 7 0.211 - 0.264: 5 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA TYR E 158 " pdb=" N TYR E 158 " pdb=" C TYR E 158 " pdb=" CB TYR E 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA TYR D 158 " pdb=" N TYR D 158 " pdb=" C TYR D 158 " pdb=" CB TYR D 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE C 306 " pdb=" CA ILE C 306 " pdb=" CG1 ILE C 306 " pdb=" CG2 ILE C 306 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1167 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 275 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C LYS B 275 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS B 275 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG B 276 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 219 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C ASN E 219 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN E 219 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE E 220 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 308 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 309 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.030 5.00e-02 4.00e+02 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2300 2.84 - 3.35: 5486 3.35 - 3.87: 11611 3.87 - 4.38: 12135 4.38 - 4.90: 22568 Nonbonded interactions: 54100 Sorted by model distance: nonbonded pdb=" OH TYR B 257 " pdb=" OE2 GLU B 299 " model vdw 2.324 3.040 nonbonded pdb=" OE1 GLU C 194 " pdb=" OH TYR C 196 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR C 135 " pdb=" O LEU C 158 " model vdw 2.349 3.040 nonbonded pdb=" O LEU A 204 " pdb=" OG SER A 208 " model vdw 2.351 3.040 nonbonded pdb=" OE1 GLU E 170 " pdb=" OH TYR E 172 " model vdw 2.392 3.040 ... (remaining 54095 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' selection = (chain 'B' and (resid 130 through 218 or resid 225 through 239 or resid 245 thro \ ugh 318)) selection = (chain 'C' and (resid 130 through 218 or resid 225 through 318)) } ncs_group { reference = (chain 'D' and (resid 108 through 134 or resid 146 through 193 or resid 206 thro \ ugh 233 or resid 238 through 291 or resid 299 through 331)) selection = chain 'E' } 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 group one per residue 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: 0.480 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.790 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: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7399 Z= 0.207 Angle : 0.909 10.852 10050 Z= 0.494 Chirality : 0.057 0.264 1170 Planarity : 0.006 0.054 1269 Dihedral : 13.913 84.215 2671 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.61 % Allowed : 5.89 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -4.05 (0.24), residues: 880 helix: -4.32 (0.26), residues: 24 sheet: -1.61 (0.27), residues: 323 loop : -3.50 (0.21), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 316 TYR 0.022 0.002 TYR A 170 PHE 0.019 0.002 PHE D 301 TRP 0.014 0.002 TRP A 134 HIS 0.005 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 ( 7399) covalent geometry : angle 0.90927 / 0.49 (10050) hydrogen bonds : bond 0.12421 / 8.51 ( 176) hydrogen bonds : angle 7.49356 / 4.99 ( 507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8376 (mttt) cc_final: 0.8081 (mtpp) REVERT: A 163 ASN cc_start: 0.8568 (t0) cc_final: 0.8292 (t0) REVERT: B 150 GLN cc_start: 0.8680 (mp-120) cc_final: 0.8340 (mt0) REVERT: D 112 GLN cc_start: 0.7804 (mt0) cc_final: 0.7533 (tt0) REVERT: D 164 LEU cc_start: 0.8553 (tp) cc_final: 0.8284 (tp) REVERT: E 208 GLN cc_start: 0.7162 (mt0) cc_final: 0.6729 (mt0) outliers start: 5 outliers final: 2 residues processed: 187 average time/residue: 0.1023 time to fit residues: 24.1489 Evaluate side-chains 124 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.5136 > 50:) chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 ASN A 151 ASN A 168 ASN A 246 HIS A 249 ASN A 302 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN D 210 GLN D 236 GLN E 126 HIS E 183 HIS E 217 ASN E 312 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.150116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129302 restraints weight = 11036.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132574 restraints weight = 6241.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134607 restraints weight = 4201.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136070 restraints weight = 3191.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136947 restraints weight = 2588.833| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7399 Z= 0.266 Angle : 0.726 7.522 10050 Z= 0.378 Chirality : 0.048 0.179 1170 Planarity : 0.005 0.039 1269 Dihedral : 6.511 35.438 973 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.48 % Favored : 88.30 % Rotamer: Outliers : 2.33 % Allowed : 14.23 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.52 (0.25), residues: 880 helix: -2.36 (0.81), residues: 19 sheet: -1.66 (0.26), residues: 343 loop : -2.93 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 180 TYR 0.019 0.002 TYR A 170 PHE 0.015 0.002 PHE C 238 TRP 0.014 0.002 TRP C 290 HIS 0.011 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.27 ( 7399) covalent geometry : angle 0.72623 / 0.38 (10050) hydrogen bonds : bond 0.03738 / 2.40 ( 176) hydrogen bonds : angle 6.43337 / 4.34 ( 507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: B 150 GLN cc_start: 0.8367 (mp-120) cc_final: 0.8079 (mt0) REVERT: C 138 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7231 (ttpt) REVERT: C 147 TYR cc_start: 0.6084 (t80) cc_final: 0.5287 (t80) REVERT: D 112 GLN cc_start: 0.7671 (mt0) cc_final: 0.7253 (tt0) outliers start: 19 outliers final: 13 residues processed: 129 average time/residue: 0.0757 time to fit residues: 13.2579 Evaluate side-chains 117 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 0.0970 chunk 8 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 246 HIS C 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.156781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137091 restraints weight = 10799.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140091 restraints weight = 6435.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141961 restraints weight = 4422.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.143162 restraints weight = 3404.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.144097 restraints weight = 2822.027| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7399 Z= 0.109 Angle : 0.588 8.644 10050 Z= 0.302 Chirality : 0.045 0.167 1170 Planarity : 0.004 0.032 1269 Dihedral : 5.657 27.104 973 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.82 % Allowed : 15.34 % Favored : 81.84 % 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: -3.00 (0.26), residues: 880 helix: -1.62 (0.97), residues: 19 sheet: -1.31 (0.27), residues: 356 loop : -2.61 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 316 TYR 0.015 0.001 TYR A 170 PHE 0.018 0.001 PHE E 247 TRP 0.013 0.002 TRP E 257 HIS 0.005 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 7399) covalent geometry : angle 0.58783 / 0.30 (10050) hydrogen bonds : bond 0.02929 / 1.86 ( 176) hydrogen bonds : angle 5.92556 / 3.98 ( 507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.278 Fit side-chains REVERT: A 162 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7739 (mtpp) REVERT: A 163 ASN cc_start: 0.8586 (t0) cc_final: 0.8299 (t0) REVERT: B 150 GLN cc_start: 0.8280 (mp-120) cc_final: 0.7953 (mt0) REVERT: E 166 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7522 (ttmm) REVERT: E 257 TRP cc_start: 0.8609 (OUTLIER) cc_final: 0.8020 (t-100) outliers start: 23 outliers final: 12 residues processed: 140 average time/residue: 0.0773 time to fit residues: 14.7474 Evaluate side-chains 122 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 257 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 63 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.156030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134999 restraints weight = 10940.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138389 restraints weight = 6191.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140447 restraints weight = 4157.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141866 restraints weight = 3146.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142853 restraints weight = 2553.262| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7399 Z= 0.129 Angle : 0.582 6.432 10050 Z= 0.300 Chirality : 0.045 0.160 1170 Planarity : 0.004 0.030 1269 Dihedral : 5.386 26.225 972 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.07 % Allowed : 15.58 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.27), residues: 880 helix: -1.31 (0.98), residues: 19 sheet: -1.16 (0.27), residues: 359 loop : -2.43 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 276 TYR 0.015 0.001 TYR A 170 PHE 0.013 0.001 PHE D 247 TRP 0.012 0.002 TRP A 134 HIS 0.003 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 7399) covalent geometry : angle 0.58193 / 0.30 (10050) hydrogen bonds : bond 0.02802 / 1.78 ( 176) hydrogen bonds : angle 5.69800 / 3.83 ( 507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.191 Fit side-chains REVERT: A 162 LYS cc_start: 0.8158 (mtmm) cc_final: 0.7734 (mtpp) REVERT: A 163 ASN cc_start: 0.8637 (t0) cc_final: 0.8352 (t0) REVERT: B 150 GLN cc_start: 0.8326 (mp-120) cc_final: 0.7989 (mt0) REVERT: C 147 TYR cc_start: 0.5806 (t80) cc_final: 0.5098 (t80) REVERT: E 257 TRP cc_start: 0.8728 (OUTLIER) cc_final: 0.8140 (t-100) outliers start: 25 outliers final: 16 residues processed: 138 average time/residue: 0.0706 time to fit residues: 13.3387 Evaluate side-chains 132 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.155066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.134283 restraints weight = 10876.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137333 restraints weight = 6224.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139494 restraints weight = 4285.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140835 restraints weight = 3228.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141828 restraints weight = 2635.604| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7399 Z= 0.150 Angle : 0.598 6.570 10050 Z= 0.307 Chirality : 0.045 0.156 1170 Planarity : 0.004 0.030 1269 Dihedral : 5.410 28.056 972 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.42 % Allowed : 15.71 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.27), residues: 880 helix: -0.99 (1.04), residues: 19 sheet: -1.12 (0.27), residues: 360 loop : -2.28 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 276 TYR 0.019 0.001 TYR B 179 PHE 0.020 0.002 PHE D 247 TRP 0.010 0.002 TRP A 134 HIS 0.003 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 7399) covalent geometry : angle 0.59751 / 0.31 (10050) hydrogen bonds : bond 0.02853 / 1.81 ( 176) hydrogen bonds : angle 5.67841 / 3.82 ( 507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.181 Fit side-chains REVERT: A 162 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7731 (mtpp) REVERT: A 163 ASN cc_start: 0.8670 (t0) cc_final: 0.8374 (t0) REVERT: B 150 GLN cc_start: 0.8237 (mp-120) cc_final: 0.7906 (mt0) REVERT: C 147 TYR cc_start: 0.5698 (t80) cc_final: 0.4983 (t80) REVERT: E 133 ASN cc_start: 0.7860 (p0) cc_final: 0.7531 (m-40) REVERT: E 166 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7687 (ttmm) REVERT: E 257 TRP cc_start: 0.8813 (OUTLIER) cc_final: 0.8237 (t-100) outliers start: 36 outliers final: 25 residues processed: 143 average time/residue: 0.0708 time to fit residues: 14.1025 Evaluate side-chains 140 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.0170 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.156384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135696 restraints weight = 10829.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138975 restraints weight = 6175.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140955 restraints weight = 4156.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.142345 restraints weight = 3148.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.143227 restraints weight = 2604.716| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7399 Z= 0.119 Angle : 0.578 6.782 10050 Z= 0.296 Chirality : 0.045 0.156 1170 Planarity : 0.004 0.030 1269 Dihedral : 5.193 25.622 972 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.42 % Allowed : 16.69 % Favored : 78.90 % 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: -2.47 (0.28), residues: 880 helix: -0.93 (1.05), residues: 19 sheet: -1.04 (0.27), residues: 358 loop : -2.17 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 243 TYR 0.014 0.001 TYR A 170 PHE 0.020 0.001 PHE D 247 TRP 0.011 0.002 TRP B 134 HIS 0.002 0.001 HIS E 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7399) covalent geometry : angle 0.57769 / 0.30 (10050) hydrogen bonds : bond 0.02691 / 1.71 ( 176) hydrogen bonds : angle 5.53828 / 3.72 ( 507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.245 Fit side-chains REVERT: A 162 LYS cc_start: 0.8153 (mtmm) cc_final: 0.7950 (mtpp) REVERT: A 163 ASN cc_start: 0.8636 (t0) cc_final: 0.8311 (t0) REVERT: B 150 GLN cc_start: 0.8246 (mp-120) cc_final: 0.7900 (mt0) REVERT: C 147 TYR cc_start: 0.5581 (t80) cc_final: 0.4884 (t80) REVERT: E 133 ASN cc_start: 0.7829 (p0) cc_final: 0.7580 (m-40) REVERT: E 166 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7689 (ttmm) REVERT: E 247 PHE cc_start: 0.8771 (t80) cc_final: 0.8544 (t80) REVERT: E 257 TRP cc_start: 0.8773 (OUTLIER) cc_final: 0.8234 (t-100) outliers start: 36 outliers final: 25 residues processed: 144 average time/residue: 0.0685 time to fit residues: 13.8896 Evaluate side-chains 136 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.153451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132089 restraints weight = 10936.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135416 restraints weight = 6173.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.137474 restraints weight = 4176.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138907 restraints weight = 3163.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139912 restraints weight = 2576.632| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7399 Z= 0.181 Angle : 0.638 7.199 10050 Z= 0.327 Chirality : 0.047 0.156 1170 Planarity : 0.004 0.034 1269 Dihedral : 5.442 28.629 972 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 4.79 % Allowed : 16.93 % Favored : 78.28 % 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: -2.50 (0.28), residues: 880 helix: -0.73 (1.11), residues: 19 sheet: -1.09 (0.28), residues: 346 loop : -2.17 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 276 TYR 0.023 0.002 TYR B 179 PHE 0.018 0.002 PHE D 247 TRP 0.018 0.002 TRP B 134 HIS 0.004 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 7399) covalent geometry : angle 0.63770 / 0.33 (10050) hydrogen bonds : bond 0.03022 / 1.93 ( 176) hydrogen bonds : angle 5.66262 / 3.80 ( 507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.241 Fit side-chains REVERT: A 162 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7697 (mtpp) REVERT: A 163 ASN cc_start: 0.8696 (t0) cc_final: 0.8379 (t0) REVERT: A 246 HIS cc_start: 0.6196 (OUTLIER) cc_final: 0.5560 (m90) REVERT: B 150 GLN cc_start: 0.8285 (mp-120) cc_final: 0.7945 (mt0) REVERT: B 248 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: E 247 PHE cc_start: 0.8783 (t80) cc_final: 0.8574 (t80) REVERT: E 257 TRP cc_start: 0.8843 (OUTLIER) cc_final: 0.8350 (t-100) outliers start: 39 outliers final: 30 residues processed: 139 average time/residue: 0.0647 time to fit residues: 12.7722 Evaluate side-chains 141 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 55 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.153990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134108 restraints weight = 10995.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136589 restraints weight = 6735.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.139462 restraints weight = 4413.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139851 restraints weight = 3224.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140016 restraints weight = 2745.974| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7399 Z= 0.151 Angle : 0.617 8.095 10050 Z= 0.315 Chirality : 0.046 0.156 1170 Planarity : 0.004 0.032 1269 Dihedral : 5.356 27.163 972 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.66 % Allowed : 17.55 % Favored : 77.79 % 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: -2.45 (0.28), residues: 880 helix: -0.77 (1.10), residues: 19 sheet: -1.07 (0.28), residues: 346 loop : -2.12 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 276 TYR 0.023 0.002 TYR B 179 PHE 0.018 0.001 PHE D 272 TRP 0.020 0.002 TRP B 134 HIS 0.003 0.001 HIS E 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 7399) covalent geometry : angle 0.61657 / 0.32 (10050) hydrogen bonds : bond 0.02875 / 1.83 ( 176) hydrogen bonds : angle 5.62746 / 3.79 ( 507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.222 Fit side-chains REVERT: A 162 LYS cc_start: 0.8315 (mtmm) cc_final: 0.7716 (mtpp) REVERT: A 163 ASN cc_start: 0.8687 (t0) cc_final: 0.8369 (t0) REVERT: A 246 HIS cc_start: 0.6315 (OUTLIER) cc_final: 0.5823 (m90) REVERT: B 150 GLN cc_start: 0.8295 (mp-120) cc_final: 0.7945 (mt0) REVERT: E 231 MET cc_start: 0.7224 (mmm) cc_final: 0.6898 (mmm) REVERT: E 247 PHE cc_start: 0.8743 (t80) cc_final: 0.8535 (t80) REVERT: E 257 TRP cc_start: 0.8834 (OUTLIER) cc_final: 0.8305 (t-100) outliers start: 38 outliers final: 30 residues processed: 135 average time/residue: 0.0632 time to fit residues: 12.2854 Evaluate side-chains 135 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 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 = 0.3949 r_free = 0.3949 target = 0.152368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132287 restraints weight = 11002.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135337 restraints weight = 6533.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137748 restraints weight = 4183.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138060 restraints weight = 3133.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138124 restraints weight = 2851.476| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7399 Z= 0.192 Angle : 0.655 7.111 10050 Z= 0.335 Chirality : 0.047 0.185 1170 Planarity : 0.004 0.034 1269 Dihedral : 5.522 28.929 972 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 4.17 % Allowed : 18.53 % Favored : 77.30 % 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: -2.54 (0.28), residues: 880 helix: -0.63 (1.15), residues: 19 sheet: -1.19 (0.28), residues: 349 loop : -2.14 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 276 TYR 0.024 0.002 TYR B 179 PHE 0.022 0.002 PHE D 272 TRP 0.026 0.002 TRP B 134 HIS 0.007 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 7399) covalent geometry : angle 0.65543 / 0.34 (10050) hydrogen bonds : bond 0.03075 / 1.96 ( 176) hydrogen bonds : angle 5.72539 / 3.87 ( 507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.214 Fit side-chains REVERT: A 162 LYS cc_start: 0.8296 (mtmm) cc_final: 0.7762 (mtpp) REVERT: B 150 GLN cc_start: 0.8215 (mp-120) cc_final: 0.7916 (mt0) REVERT: E 247 PHE cc_start: 0.8714 (t80) cc_final: 0.8507 (t80) REVERT: E 257 TRP cc_start: 0.8874 (OUTLIER) cc_final: 0.8390 (t-100) outliers start: 34 outliers final: 30 residues processed: 132 average time/residue: 0.0707 time to fit residues: 13.0294 Evaluate side-chains 138 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 68 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 29 optimal weight: 0.0040 chunk 64 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN ** C 130 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 = 0.3975 r_free = 0.3975 target = 0.154503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133275 restraints weight = 10943.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136648 restraints weight = 6198.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138692 restraints weight = 4190.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140196 restraints weight = 3177.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141159 restraints weight = 2581.224| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7399 Z= 0.149 Angle : 0.639 11.888 10050 Z= 0.322 Chirality : 0.046 0.163 1170 Planarity : 0.004 0.032 1269 Dihedral : 5.389 26.852 972 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.17 % Allowed : 19.14 % Favored : 76.69 % 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: -2.48 (0.28), residues: 880 helix: -0.80 (1.10), residues: 19 sheet: -1.12 (0.27), residues: 351 loop : -2.12 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 276 TYR 0.023 0.001 TYR B 179 PHE 0.021 0.002 PHE D 272 TRP 0.025 0.002 TRP B 134 HIS 0.002 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 7399) covalent geometry : angle 0.63933 / 0.32 (10050) hydrogen bonds : bond 0.02880 / 1.85 ( 176) hydrogen bonds : angle 5.65106 / 3.81 ( 507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8311 (mtmm) cc_final: 0.7717 (mtpp) REVERT: A 163 ASN cc_start: 0.8681 (t0) cc_final: 0.8368 (t0) REVERT: B 150 GLN cc_start: 0.8203 (mp-120) cc_final: 0.7883 (mt0) REVERT: C 213 ASP cc_start: 0.8373 (t0) cc_final: 0.8122 (t0) REVERT: D 183 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.6581 (m-70) REVERT: E 231 MET cc_start: 0.7426 (mmm) cc_final: 0.7020 (mmm) REVERT: E 257 TRP cc_start: 0.8834 (OUTLIER) cc_final: 0.8275 (t-100) outliers start: 34 outliers final: 31 residues processed: 131 average time/residue: 0.0636 time to fit residues: 11.9574 Evaluate side-chains 136 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 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 = 0.3937 r_free = 0.3937 target = 0.151355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.131028 restraints weight = 11115.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134071 restraints weight = 6641.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136821 restraints weight = 4253.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137068 restraints weight = 3116.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137159 restraints weight = 2816.957| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7399 Z= 0.208 Angle : 0.686 9.391 10050 Z= 0.349 Chirality : 0.048 0.167 1170 Planarity : 0.004 0.033 1269 Dihedral : 5.634 30.378 972 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 4.91 % Allowed : 18.28 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.55 (0.28), residues: 880 helix: -0.51 (1.17), residues: 19 sheet: -1.10 (0.27), residues: 354 loop : -2.24 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 150 TYR 0.021 0.002 TYR B 179 PHE 0.021 0.002 PHE E 247 TRP 0.027 0.002 TRP B 134 HIS 0.002 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 ( 7399) covalent geometry : angle 0.68629 / 0.35 (10050) hydrogen bonds : bond 0.03184 / 2.03 ( 176) hydrogen bonds : angle 5.83230 / 3.94 ( 507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1056.22 seconds wall clock time: 18 minutes 58.16 seconds (1138.16 seconds total)