Starting phenix.real_space_refine on Wed Sep 17 08:39:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gqz_51515/09_2025/9gqz_51515.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gqz_51515/09_2025/9gqz_51515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gqz_51515/09_2025/9gqz_51515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gqz_51515/09_2025/9gqz_51515.map" model { file = "/net/cci-nas-00/data/ceres_data/9gqz_51515/09_2025/9gqz_51515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gqz_51515/09_2025/9gqz_51515.cif" } resolution = 2.36 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= 0.010 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 8 5.49 5 S 24 5.16 5 C 4623 2.51 5 N 1298 2.21 5 O 1378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7331 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 162 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "F" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 185 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "B" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3389 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 20, 'TRANS': 416} Chain breaks: 1 Chain: "C" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3384 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Chain: "B" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FAD': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FAD': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 2.04, per 1000 atoms: 0.28 Number of scatterers: 7331 At special positions: 0 Unit cell: (85.674, 87.636, 113.796, 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 24 16.00 P 8 15.00 O 1378 8.00 N 1298 7.00 C 4623 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: 0.55 Conformation dependent library (CDL) restraints added in 407.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1652 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 16 sheets defined 30.9% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'F' and resid 16 through 22 Processing helix chain 'B' and resid 140 through 154 Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.880A pdb=" N SER B 176 " --> pdb=" O ARG B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 267 through 274 removed outlier: 3.942A pdb=" N GLY B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 309 through 327 Processing helix chain 'B' and resid 345 through 359 Processing helix chain 'B' and resid 404 through 411 removed outlier: 4.325A pdb=" N LYS B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 470 Processing helix chain 'B' and resid 584 through 594 Processing helix chain 'B' and resid 601 through 607 removed outlier: 3.625A pdb=" N LEU B 607 " --> pdb=" O GLU B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 154 Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.894A pdb=" N SER C 176 " --> pdb=" O ARG C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 removed outlier: 4.104A pdb=" N PHE C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 267 through 273 Processing helix chain 'C' and resid 274 through 280 removed outlier: 3.624A pdb=" N LYS C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 309 through 327 Processing helix chain 'C' and resid 345 through 359 Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.963A pdb=" N LYS C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 471 Processing helix chain 'C' and resid 584 through 594 removed outlier: 3.550A pdb=" N ALA C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 606 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AA3, first strand: chain 'B' and resid 224 through 229 removed outlier: 7.909A pdb=" N ARG B 158 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N HIS B 131 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR B 253 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 229 removed outlier: 7.909A pdb=" N ARG B 158 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N HIS B 131 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR B 253 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 192 through 194 Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AA7, first strand: chain 'B' and resid 281 through 283 removed outlier: 6.954A pdb=" N SER B 302 " --> pdb=" O HIS B 393 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL B 395 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR B 304 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL B 330 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N MET B 364 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN B 332 " --> pdb=" O MET B 364 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 375 Processing sheet with id=AA9, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.050A pdb=" N PHE B 421 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N TYR B 443 " --> pdb=" O PHE B 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 224 through 229 removed outlier: 6.524A pdb=" N VAL C 159 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU C 228 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE C 161 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ARG C 158 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N HIS C 131 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N LYS C 255 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU C 257 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 135 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 224 through 229 removed outlier: 6.524A pdb=" N VAL C 159 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU C 228 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE C 161 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ARG C 158 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N HIS C 131 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N LYS C 255 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU C 257 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 135 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE C 433 " --> pdb=" O ALA C 429 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 192 through 194 Processing sheet with id=AB4, first strand: chain 'C' and resid 262 through 264 Processing sheet with id=AB5, first strand: chain 'C' and resid 281 through 282 removed outlier: 6.614A pdb=" N THR C 282 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C 330 " --> pdb=" O LYS C 362 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N MET C 364 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN C 332 " --> pdb=" O MET C 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 369 through 375 Processing sheet with id=AB7, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.034A pdb=" N PHE C 421 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N TYR C 443 " --> pdb=" O PHE C 421 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 930 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: 1.16 Time building geometry restraints manager: 0.73 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: 1539 1.33 - 1.45: 1682 1.45 - 1.57: 4198 1.57 - 1.69: 16 1.69 - 1.81: 40 Bond restraints: 7475 Sorted by residual: bond pdb=" C MET B 585 " pdb=" O MET B 585 " ideal model delta sigma weight residual 1.244 1.234 0.009 9.80e-03 1.04e+04 9.10e-01 bond pdb=" N PRO B 173 " pdb=" CA PRO B 173 " ideal model delta sigma weight residual 1.465 1.484 -0.019 2.03e-02 2.43e+03 8.93e-01 bond pdb=" N PRO C 173 " pdb=" CA PRO C 173 " ideal model delta sigma weight residual 1.465 1.482 -0.018 2.03e-02 2.43e+03 7.47e-01 bond pdb=" N GLY C 140 " pdb=" CA GLY C 140 " ideal model delta sigma weight residual 1.450 1.442 0.007 9.10e-03 1.21e+04 6.75e-01 bond pdb=" CA ALA B 128 " pdb=" C ALA B 128 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.10e-02 2.27e+03 6.07e-01 ... (remaining 7470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 9880 1.30 - 2.59: 184 2.59 - 3.89: 46 3.89 - 5.18: 11 5.18 - 6.48: 5 Bond angle restraints: 10126 Sorted by residual: angle pdb=" N VAL B 574 " pdb=" CA VAL B 574 " pdb=" C VAL B 574 " ideal model delta sigma weight residual 112.96 109.78 3.18 1.00e+00 1.00e+00 1.01e+01 angle pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" C ARG C 172 " ideal model delta sigma weight residual 109.81 116.29 -6.48 2.21e+00 2.05e-01 8.59e+00 angle pdb=" N PRO B 173 " pdb=" CA PRO B 173 " pdb=" C PRO B 173 " ideal model delta sigma weight residual 110.70 114.15 -3.45 1.22e+00 6.72e-01 7.98e+00 angle pdb=" N ARG B 172 " pdb=" CA ARG B 172 " pdb=" C ARG B 172 " ideal model delta sigma weight residual 109.81 115.87 -6.06 2.21e+00 2.05e-01 7.52e+00 angle pdb=" N PRO C 173 " pdb=" CA PRO C 173 " pdb=" C PRO C 173 " ideal model delta sigma weight residual 110.70 113.74 -3.04 1.22e+00 6.72e-01 6.21e+00 ... (remaining 10121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4140 17.73 - 35.46: 322 35.46 - 53.19: 87 53.19 - 70.92: 11 70.92 - 88.65: 7 Dihedral angle restraints: 4567 sinusoidal: 1985 harmonic: 2582 Sorted by residual: dihedral pdb=" CA LYS B 177 " pdb=" C LYS B 177 " pdb=" N GLU B 178 " pdb=" CA GLU B 178 " ideal model delta harmonic sigma weight residual 180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ARG C 450 " pdb=" C ARG C 450 " pdb=" N ARG C 451 " pdb=" CA ARG C 451 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA LYS C 177 " pdb=" C LYS C 177 " pdb=" N GLU C 178 " pdb=" CA GLU C 178 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 4564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 562 0.024 - 0.048: 306 0.048 - 0.073: 107 0.073 - 0.097: 65 0.097 - 0.121: 69 Chirality restraints: 1109 Sorted by residual: chirality pdb=" CA ILE B 303 " pdb=" N ILE B 303 " pdb=" C ILE B 303 " pdb=" CB ILE B 303 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA ARG C 239 " pdb=" N ARG C 239 " pdb=" C ARG C 239 " pdb=" CB ARG C 239 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ILE C 331 " pdb=" N ILE C 331 " pdb=" C ILE C 331 " pdb=" CB ILE C 331 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 1106 not shown) Planarity restraints: 1277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 174 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C PRO B 174 " 0.030 2.00e-02 2.50e+03 pdb=" O PRO B 174 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 175 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 174 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C PRO C 174 " -0.029 2.00e-02 2.50e+03 pdb=" O PRO C 174 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU C 175 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 585 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO C 586 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 586 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 586 " -0.023 5.00e-02 4.00e+02 ... (remaining 1274 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 295 2.72 - 3.27: 7074 3.27 - 3.81: 12504 3.81 - 4.36: 16039 4.36 - 4.90: 26720 Nonbonded interactions: 62632 Sorted by model distance: nonbonded pdb=" O1N NAD B 702 " pdb=" O HOH B 801 " model vdw 2.177 3.040 nonbonded pdb=" OD2 ASP B 499 " pdb=" OG SER B 501 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP F 10 " pdb=" OG1 THR C 504 " model vdw 2.239 3.040 nonbonded pdb=" NH2 ARG C 272 " pdb=" O GLN C 370 " model vdw 2.275 3.120 nonbonded pdb=" O GLY C 138 " pdb=" O HOH C 801 " model vdw 2.285 3.040 ... (remaining 62627 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 'F' and resid 2 through 20) } ncs_group { reference = (chain 'B' and resid 129 through 702) selection = chain 'C' } 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.540 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.002 0.034 7475 Z= 0.111 Angle : 0.499 6.476 10126 Z= 0.264 Chirality : 0.044 0.121 1109 Planarity : 0.004 0.047 1277 Dihedral : 13.894 88.651 2915 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % 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 aren not related in a simple way. whole: 0.40 (0.28), residues: 902 helix: 1.78 (0.34), residues: 235 sheet: 0.13 (0.35), residues: 221 loop : -0.45 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 239 TYR 0.021 0.001 TYR C 492 PHE 0.011 0.001 PHE B 418 TRP 0.011 0.001 TRP C 351 HIS 0.004 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7475) covalent geometry : angle 0.49931 (10126) hydrogen bonds : bond 0.15724 ( 305) hydrogen bonds : angle 7.37953 ( 930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.7083 time to fit residues: 114.6841 Evaluate side-chains 96 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.0010 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 197 ASN B 206 GLN B 597 GLN C 206 GLN C 370 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.101988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.081901 restraints weight = 13102.910| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.02 r_work: 0.3108 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7475 Z= 0.122 Angle : 0.552 6.560 10126 Z= 0.291 Chirality : 0.045 0.158 1109 Planarity : 0.004 0.054 1277 Dihedral : 6.333 40.412 1194 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.70 % Allowed : 18.10 % Favored : 78.20 % 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 aren not related in a simple way. whole: 0.46 (0.28), residues: 902 helix: 1.89 (0.34), residues: 242 sheet: 0.17 (0.34), residues: 241 loop : -0.51 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 463 TYR 0.014 0.001 TYR C 567 PHE 0.012 0.001 PHE B 482 TRP 0.010 0.001 TRP C 351 HIS 0.004 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7475) covalent geometry : angle 0.55250 (10126) hydrogen bonds : bond 0.03855 ( 305) hydrogen bonds : angle 5.64194 ( 930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7558 (ttt90) REVERT: B 242 MET cc_start: 0.8431 (ttt) cc_final: 0.8116 (ttp) REVERT: B 250 GLN cc_start: 0.8838 (mt0) cc_final: 0.8566 (tt0) REVERT: B 299 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8664 (mt-10) REVERT: B 401 GLU cc_start: 0.8098 (tp30) cc_final: 0.7671 (tm-30) REVERT: B 499 ASP cc_start: 0.8390 (t0) cc_final: 0.8087 (t0) REVERT: B 571 LYS cc_start: 0.8890 (mttp) cc_final: 0.8456 (ttmt) REVERT: B 597 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: B 604 VAL cc_start: 0.8755 (m) cc_final: 0.8489 (p) REVERT: C 340 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7305 (mpp) REVERT: C 385 ASP cc_start: 0.8605 (t0) cc_final: 0.8347 (t0) REVERT: C 408 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8595 (mtmm) REVERT: C 499 ASP cc_start: 0.8209 (t0) cc_final: 0.7938 (t0) REVERT: C 596 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7716 (mp0) outliers start: 28 outliers final: 7 residues processed: 137 average time/residue: 0.6600 time to fit residues: 94.9288 Evaluate side-chains 102 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 597 GLN Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 609 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN C 206 GLN C 370 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.095694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.075435 restraints weight = 13463.318| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.04 r_work: 0.3007 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 7475 Z= 0.269 Angle : 0.619 7.795 10126 Z= 0.324 Chirality : 0.047 0.154 1109 Planarity : 0.005 0.061 1277 Dihedral : 6.988 40.509 1194 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.70 % Allowed : 19.15 % Favored : 77.15 % 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 aren not related in a simple way. whole: 0.25 (0.28), residues: 902 helix: 1.80 (0.34), residues: 242 sheet: -0.14 (0.32), residues: 245 loop : -0.56 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 158 TYR 0.022 0.002 TYR C 567 PHE 0.014 0.002 PHE B 482 TRP 0.009 0.001 TRP B 579 HIS 0.008 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 7475) covalent geometry : angle 0.61869 (10126) hydrogen bonds : bond 0.04475 ( 305) hydrogen bonds : angle 5.73919 ( 930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8782 (ptpp) cc_final: 0.8327 (ttpp) REVERT: B 242 MET cc_start: 0.8593 (ttt) cc_final: 0.8123 (ttt) REVERT: B 390 GLU cc_start: 0.8378 (tp30) cc_final: 0.8169 (tm-30) REVERT: B 401 GLU cc_start: 0.8267 (tp30) cc_final: 0.7828 (tm-30) REVERT: B 499 ASP cc_start: 0.8516 (t0) cc_final: 0.8127 (t0) REVERT: B 571 LYS cc_start: 0.8944 (mttp) cc_final: 0.8403 (ttmt) REVERT: B 604 VAL cc_start: 0.8930 (m) cc_final: 0.8705 (p) REVERT: C 177 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8283 (ttmt) REVERT: C 186 ASN cc_start: 0.9014 (m-40) cc_final: 0.8763 (t0) REVERT: C 272 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6544 (ptt-90) REVERT: C 340 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7359 (mpp) REVERT: C 370 GLN cc_start: 0.8285 (tt0) cc_final: 0.8023 (tt0) REVERT: C 385 ASP cc_start: 0.8757 (t0) cc_final: 0.8394 (t0) REVERT: C 596 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: C 609 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8040 (p0) outliers start: 28 outliers final: 11 residues processed: 117 average time/residue: 0.6724 time to fit residues: 82.7985 Evaluate side-chains 101 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 609 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN B 235 GLN C 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.096760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.076550 restraints weight = 13525.525| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.06 r_work: 0.3030 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7475 Z= 0.194 Angle : 0.573 6.872 10126 Z= 0.301 Chirality : 0.046 0.163 1109 Planarity : 0.004 0.058 1277 Dihedral : 6.637 39.795 1194 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.57 % Allowed : 19.15 % Favored : 77.28 % 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 aren not related in a simple way. whole: 0.28 (0.28), residues: 902 helix: 1.87 (0.34), residues: 243 sheet: -0.15 (0.32), residues: 245 loop : -0.57 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 201 TYR 0.014 0.002 TYR B 476 PHE 0.011 0.001 PHE B 482 TRP 0.008 0.001 TRP C 351 HIS 0.006 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 7475) covalent geometry : angle 0.57257 (10126) hydrogen bonds : bond 0.03910 ( 305) hydrogen bonds : angle 5.47213 ( 930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8777 (ptpp) cc_final: 0.8229 (ttpp) REVERT: B 141 THR cc_start: 0.8991 (m) cc_final: 0.8773 (p) REVERT: B 242 MET cc_start: 0.8542 (ttt) cc_final: 0.8034 (ttt) REVERT: B 401 GLU cc_start: 0.8284 (tp30) cc_final: 0.7889 (tm-30) REVERT: B 499 ASP cc_start: 0.8495 (t0) cc_final: 0.8058 (t0) REVERT: B 604 VAL cc_start: 0.8938 (m) cc_final: 0.8724 (p) REVERT: C 186 ASN cc_start: 0.9038 (m-40) cc_final: 0.8770 (t0) REVERT: C 216 ASP cc_start: 0.8927 (m-30) cc_final: 0.8522 (p0) REVERT: C 237 ASP cc_start: 0.8758 (t70) cc_final: 0.8456 (t0) REVERT: C 272 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6455 (ptt-90) REVERT: C 340 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7486 (mpp) REVERT: C 370 GLN cc_start: 0.8280 (tt0) cc_final: 0.7991 (tt0) REVERT: C 385 ASP cc_start: 0.8816 (t0) cc_final: 0.8453 (t0) REVERT: C 596 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7831 (mp0) outliers start: 27 outliers final: 11 residues processed: 117 average time/residue: 0.5955 time to fit residues: 73.4452 Evaluate side-chains 102 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 609 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN B 235 GLN C 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.098689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078795 restraints weight = 13328.392| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.08 r_work: 0.3070 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7475 Z= 0.130 Angle : 0.547 6.677 10126 Z= 0.288 Chirality : 0.045 0.165 1109 Planarity : 0.004 0.058 1277 Dihedral : 6.354 39.568 1194 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.77 % Allowed : 20.48 % Favored : 76.75 % 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 aren not related in a simple way. whole: 0.40 (0.28), residues: 902 helix: 2.08 (0.35), residues: 242 sheet: -0.08 (0.32), residues: 245 loop : -0.57 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 201 TYR 0.010 0.001 TYR B 476 PHE 0.011 0.001 PHE B 482 TRP 0.009 0.001 TRP C 351 HIS 0.005 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7475) covalent geometry : angle 0.54696 (10126) hydrogen bonds : bond 0.03448 ( 305) hydrogen bonds : angle 5.24080 ( 930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8792 (ptpp) cc_final: 0.8382 (ttpp) REVERT: A 10 ASP cc_start: 0.8164 (m-30) cc_final: 0.7605 (p0) REVERT: B 242 MET cc_start: 0.8489 (ttt) cc_final: 0.8063 (ttt) REVERT: B 401 GLU cc_start: 0.8279 (tp30) cc_final: 0.7924 (tm-30) REVERT: B 481 MET cc_start: 0.8615 (ppp) cc_final: 0.8053 (ppp) REVERT: B 499 ASP cc_start: 0.8474 (t0) cc_final: 0.8006 (t0) REVERT: C 186 ASN cc_start: 0.9058 (m-40) cc_final: 0.8810 (t0) REVERT: C 216 ASP cc_start: 0.8896 (m-30) cc_final: 0.8478 (p0) REVERT: C 220 ILE cc_start: 0.8361 (pt) cc_final: 0.8081 (pp) REVERT: C 237 ASP cc_start: 0.8728 (t70) cc_final: 0.8439 (t0) REVERT: C 272 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6397 (ptt-90) REVERT: C 340 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7411 (mpp) REVERT: C 370 GLN cc_start: 0.8260 (tt0) cc_final: 0.7970 (tt0) REVERT: C 385 ASP cc_start: 0.8838 (t0) cc_final: 0.8437 (t0) REVERT: C 596 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7867 (mp0) outliers start: 21 outliers final: 11 residues processed: 113 average time/residue: 0.5995 time to fit residues: 71.4684 Evaluate side-chains 94 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 609 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 80 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN B 250 GLN B 597 GLN C 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.097045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.076958 restraints weight = 13456.323| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.07 r_work: 0.3042 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7475 Z= 0.182 Angle : 0.563 6.820 10126 Z= 0.296 Chirality : 0.046 0.169 1109 Planarity : 0.004 0.060 1277 Dihedral : 6.501 39.233 1194 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.17 % Allowed : 20.61 % Favored : 76.22 % 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 aren not related in a simple way. whole: 0.36 (0.29), residues: 902 helix: 2.02 (0.34), residues: 242 sheet: -0.04 (0.32), residues: 245 loop : -0.61 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 201 TYR 0.016 0.002 TYR C 567 PHE 0.011 0.001 PHE B 482 TRP 0.008 0.001 TRP C 351 HIS 0.006 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 7475) covalent geometry : angle 0.56337 (10126) hydrogen bonds : bond 0.03730 ( 305) hydrogen bonds : angle 5.28390 ( 930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8781 (ptpp) cc_final: 0.8180 (ttpp) REVERT: F 5 ARG cc_start: 0.8121 (ttp-170) cc_final: 0.7327 (ttp80) REVERT: B 242 MET cc_start: 0.8493 (ttt) cc_final: 0.8071 (ttt) REVERT: B 336 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: B 401 GLU cc_start: 0.8305 (tp30) cc_final: 0.7979 (tm-30) REVERT: B 481 MET cc_start: 0.8637 (ppp) cc_final: 0.7940 (ppp) REVERT: B 499 ASP cc_start: 0.8509 (t0) cc_final: 0.8080 (t0) REVERT: B 596 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7560 (tm-30) REVERT: C 186 ASN cc_start: 0.9067 (m-40) cc_final: 0.8815 (t0) REVERT: C 216 ASP cc_start: 0.8940 (m-30) cc_final: 0.8479 (p0) REVERT: C 220 ILE cc_start: 0.8367 (pt) cc_final: 0.8069 (pp) REVERT: C 237 ASP cc_start: 0.8752 (t0) cc_final: 0.8409 (t0) REVERT: C 385 ASP cc_start: 0.8841 (t0) cc_final: 0.8466 (t0) REVERT: C 596 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7894 (mp0) outliers start: 24 outliers final: 11 residues processed: 104 average time/residue: 0.6397 time to fit residues: 70.1816 Evaluate side-chains 93 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 609 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.096587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.076801 restraints weight = 13594.897| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.06 r_work: 0.3035 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7475 Z= 0.195 Angle : 0.577 6.884 10126 Z= 0.303 Chirality : 0.046 0.171 1109 Planarity : 0.004 0.060 1277 Dihedral : 6.548 39.053 1194 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.77 % Allowed : 22.46 % Favored : 74.77 % 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 aren not related in a simple way. whole: 0.31 (0.29), residues: 902 helix: 1.98 (0.34), residues: 242 sheet: -0.07 (0.32), residues: 245 loop : -0.65 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 201 TYR 0.026 0.002 TYR C 567 PHE 0.011 0.001 PHE B 482 TRP 0.008 0.001 TRP C 180 HIS 0.006 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 7475) covalent geometry : angle 0.57668 (10126) hydrogen bonds : bond 0.03762 ( 305) hydrogen bonds : angle 5.33368 ( 930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8788 (ptpp) cc_final: 0.8145 (ttpp) REVERT: F 5 ARG cc_start: 0.8106 (ttp-170) cc_final: 0.7312 (ttp80) REVERT: B 242 MET cc_start: 0.8462 (ttt) cc_final: 0.8126 (ttt) REVERT: B 336 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: B 401 GLU cc_start: 0.8336 (tp30) cc_final: 0.8015 (tm-30) REVERT: B 481 MET cc_start: 0.8657 (ppp) cc_final: 0.7954 (ppp) REVERT: B 499 ASP cc_start: 0.8556 (t0) cc_final: 0.8108 (t0) REVERT: C 186 ASN cc_start: 0.9073 (m-40) cc_final: 0.8823 (t0) REVERT: C 216 ASP cc_start: 0.8966 (m-30) cc_final: 0.8476 (p0) REVERT: C 220 ILE cc_start: 0.8381 (pt) cc_final: 0.8097 (pp) REVERT: C 237 ASP cc_start: 0.8746 (t0) cc_final: 0.8393 (t0) REVERT: C 272 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6645 (ptt-90) REVERT: C 385 ASP cc_start: 0.8839 (t0) cc_final: 0.8444 (t0) REVERT: C 596 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7886 (mp0) outliers start: 21 outliers final: 13 residues processed: 104 average time/residue: 0.6531 time to fit residues: 71.5389 Evaluate side-chains 97 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 609 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 GLN C 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.095937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.076643 restraints weight = 14175.234| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.06 r_work: 0.3119 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7475 Z= 0.207 Angle : 0.594 7.099 10126 Z= 0.314 Chirality : 0.046 0.170 1109 Planarity : 0.004 0.061 1277 Dihedral : 6.618 39.258 1194 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.30 % Allowed : 22.46 % Favored : 74.24 % 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 aren not related in a simple way. whole: 0.28 (0.29), residues: 902 helix: 1.95 (0.34), residues: 242 sheet: -0.09 (0.32), residues: 245 loop : -0.67 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 201 TYR 0.034 0.002 TYR C 567 PHE 0.011 0.001 PHE B 482 TRP 0.008 0.001 TRP C 579 HIS 0.007 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 7475) covalent geometry : angle 0.59358 (10126) hydrogen bonds : bond 0.03836 ( 305) hydrogen bonds : angle 5.40661 ( 930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8199 (m-30) cc_final: 0.7674 (p0) REVERT: F 5 ARG cc_start: 0.8097 (ttp-170) cc_final: 0.7315 (ttp80) REVERT: B 242 MET cc_start: 0.8499 (ttt) cc_final: 0.8116 (ttt) REVERT: B 336 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: B 388 LYS cc_start: 0.8730 (tppt) cc_final: 0.8508 (tppp) REVERT: B 401 GLU cc_start: 0.8348 (tp30) cc_final: 0.8056 (tm-30) REVERT: B 481 MET cc_start: 0.8657 (ppp) cc_final: 0.7988 (ppp) REVERT: B 499 ASP cc_start: 0.8638 (t0) cc_final: 0.8222 (t0) REVERT: C 186 ASN cc_start: 0.9099 (m-40) cc_final: 0.8843 (t0) REVERT: C 216 ASP cc_start: 0.8964 (m-30) cc_final: 0.8466 (p0) REVERT: C 237 ASP cc_start: 0.8794 (t0) cc_final: 0.8430 (t0) REVERT: C 272 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6705 (ptt-90) REVERT: C 385 ASP cc_start: 0.8783 (t0) cc_final: 0.8403 (t0) REVERT: C 596 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7822 (mp0) outliers start: 25 outliers final: 12 residues processed: 102 average time/residue: 0.6291 time to fit residues: 67.6237 Evaluate side-chains 98 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 609 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.095979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.076503 restraints weight = 13834.663| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.05 r_work: 0.3138 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7475 Z= 0.196 Angle : 0.595 6.922 10126 Z= 0.314 Chirality : 0.046 0.166 1109 Planarity : 0.004 0.061 1277 Dihedral : 6.607 39.914 1194 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.51 % Allowed : 23.25 % Favored : 74.24 % 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 aren not related in a simple way. whole: 0.28 (0.29), residues: 902 helix: 1.93 (0.34), residues: 243 sheet: -0.08 (0.32), residues: 245 loop : -0.66 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 201 TYR 0.034 0.002 TYR C 567 PHE 0.012 0.001 PHE B 482 TRP 0.015 0.001 TRP C 180 HIS 0.006 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 7475) covalent geometry : angle 0.59521 (10126) hydrogen bonds : bond 0.03790 ( 305) hydrogen bonds : angle 5.39975 ( 930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8807 (ptpp) cc_final: 0.8404 (ttpp) REVERT: F 5 ARG cc_start: 0.8074 (ttp-170) cc_final: 0.7293 (ttp80) REVERT: B 242 MET cc_start: 0.8533 (ttt) cc_final: 0.8127 (ttt) REVERT: B 336 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: B 388 LYS cc_start: 0.8737 (tppt) cc_final: 0.8528 (tppp) REVERT: B 401 GLU cc_start: 0.8365 (tp30) cc_final: 0.8104 (tm-30) REVERT: B 481 MET cc_start: 0.8631 (ppp) cc_final: 0.7863 (ppp) REVERT: B 499 ASP cc_start: 0.8664 (t0) cc_final: 0.8226 (t0) REVERT: B 571 LYS cc_start: 0.8774 (mttp) cc_final: 0.8230 (ttmm) REVERT: C 186 ASN cc_start: 0.9110 (m-40) cc_final: 0.8859 (t0) REVERT: C 216 ASP cc_start: 0.8934 (m-30) cc_final: 0.8500 (p0) REVERT: C 237 ASP cc_start: 0.8791 (t0) cc_final: 0.8450 (t0) REVERT: C 272 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6752 (ptt-90) REVERT: C 385 ASP cc_start: 0.8762 (t0) cc_final: 0.8442 (t0) REVERT: C 596 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7845 (mp0) outliers start: 19 outliers final: 12 residues processed: 101 average time/residue: 0.6266 time to fit residues: 66.7346 Evaluate side-chains 97 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 609 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.078910 restraints weight = 13617.287| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.07 r_work: 0.3068 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7475 Z= 0.132 Angle : 0.567 7.305 10126 Z= 0.297 Chirality : 0.046 0.184 1109 Planarity : 0.004 0.059 1277 Dihedral : 6.284 40.117 1194 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.98 % Allowed : 24.17 % Favored : 73.84 % 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 aren not related in a simple way. whole: 0.34 (0.29), residues: 902 helix: 2.01 (0.35), residues: 243 sheet: -0.03 (0.33), residues: 245 loop : -0.66 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 201 TYR 0.025 0.002 TYR C 567 PHE 0.025 0.001 PHE C 181 TRP 0.012 0.001 TRP C 579 HIS 0.004 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7475) covalent geometry : angle 0.56737 (10126) hydrogen bonds : bond 0.03366 ( 305) hydrogen bonds : angle 5.22962 ( 930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8793 (ptpp) cc_final: 0.8563 (ttpp) REVERT: A 10 ASP cc_start: 0.8181 (m-30) cc_final: 0.7660 (p0) REVERT: B 242 MET cc_start: 0.8411 (ttt) cc_final: 0.8019 (ttt) REVERT: B 336 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: B 388 LYS cc_start: 0.8747 (tppt) cc_final: 0.8537 (tppp) REVERT: B 401 GLU cc_start: 0.8286 (tp30) cc_final: 0.7905 (pp20) REVERT: B 481 MET cc_start: 0.8543 (ppp) cc_final: 0.7776 (ppp) REVERT: B 499 ASP cc_start: 0.8579 (t0) cc_final: 0.8192 (t0) REVERT: C 186 ASN cc_start: 0.9081 (m-40) cc_final: 0.8820 (t0) REVERT: C 216 ASP cc_start: 0.8909 (m-30) cc_final: 0.8496 (p0) REVERT: C 237 ASP cc_start: 0.8742 (t0) cc_final: 0.8475 (t0) REVERT: C 385 ASP cc_start: 0.8757 (t0) cc_final: 0.8432 (t0) REVERT: C 596 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7881 (mp0) outliers start: 15 outliers final: 9 residues processed: 106 average time/residue: 0.5689 time to fit residues: 63.7775 Evaluate side-chains 99 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 609 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.096893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.076910 restraints weight = 13692.141| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.08 r_work: 0.3036 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7475 Z= 0.176 Angle : 0.592 7.155 10126 Z= 0.313 Chirality : 0.046 0.190 1109 Planarity : 0.004 0.061 1277 Dihedral : 6.643 42.166 1194 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.72 % Allowed : 24.70 % Favored : 73.58 % 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 aren not related in a simple way. whole: 0.30 (0.29), residues: 902 helix: 1.91 (0.34), residues: 243 sheet: -0.01 (0.33), residues: 245 loop : -0.66 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 201 TYR 0.038 0.002 TYR C 567 PHE 0.012 0.001 PHE B 482 TRP 0.008 0.001 TRP C 351 HIS 0.006 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 7475) covalent geometry : angle 0.59180 (10126) hydrogen bonds : bond 0.03629 ( 305) hydrogen bonds : angle 5.33071 ( 930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.22 seconds wall clock time: 52 minutes 2.38 seconds (3122.38 seconds total)