Starting phenix.real_space_refine on Fri Jul 25 07:08:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gqz_51515/07_2025/9gqz_51515.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gqz_51515/07_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_51515/07_2025/9gqz_51515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gqz_51515/07_2025/9gqz_51515.map" model { file = "/net/cci-nas-00/data/ceres_data/9gqz_51515/07_2025/9gqz_51515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gqz_51515/07_2025/9gqz_51515.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.32, per 1000 atoms: 0.73 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: 1.97 Conformation dependent library (CDL) restraints added in 902.0 milliseconds 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: 1.01 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: 2.55 Time building geometry restraints manager: 2.32 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 611 or resid 701 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: 1.680 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.960 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.740 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP C 351 HIS 0.004 0.001 HIS B 457 PHE 0.011 0.001 PHE B 418 TYR 0.021 0.001 TYR C 492 ARG 0.009 0.000 ARG C 239 Details of bonding type rmsd hydrogen bonds : bond 0.15724 ( 305) hydrogen bonds : angle 7.37953 ( 930) covalent geometry : bond 0.00240 ( 7475) covalent geometry : angle 0.49931 (10126) *********************** 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 : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 1.3962 time to fit residues: 226.7458 Evaluate side-chains 97 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 0.0770 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.096953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.076875 restraints weight = 13251.011| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.00 r_work: 0.3025 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 7475 Z= 0.227 Angle : 0.603 6.534 10126 Z= 0.317 Chirality : 0.047 0.162 1109 Planarity : 0.005 0.054 1277 Dihedral : 6.825 41.173 1194 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.49 % Allowed : 17.70 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.28), residues: 902 helix: 1.76 (0.33), residues: 242 sheet: 0.06 (0.33), residues: 239 loop : -0.60 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 351 HIS 0.007 0.001 HIS B 457 PHE 0.017 0.002 PHE B 482 TYR 0.011 0.002 TYR C 567 ARG 0.006 0.001 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.04576 ( 305) hydrogen bonds : angle 5.87092 ( 930) covalent geometry : bond 0.00529 ( 7475) covalent geometry : angle 0.60259 (10126) *********************** 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 138 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7622 (ttt90) REVERT: B 189 LYS cc_start: 0.9323 (mtmt) cc_final: 0.9107 (mtmm) REVERT: B 242 MET cc_start: 0.8624 (ttt) cc_final: 0.8240 (ttt) REVERT: B 296 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9071 (mp) REVERT: B 299 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8273 (mt-10) REVERT: B 401 GLU cc_start: 0.8166 (tp30) cc_final: 0.7785 (tm-30) REVERT: B 499 ASP cc_start: 0.8518 (t0) cc_final: 0.8208 (t0) REVERT: B 571 LYS cc_start: 0.8908 (mttp) cc_final: 0.8369 (ttmt) REVERT: B 597 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: B 604 VAL cc_start: 0.8862 (m) cc_final: 0.8617 (p) REVERT: C 177 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8293 (ttmt) REVERT: C 340 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7357 (mpp) REVERT: C 385 ASP cc_start: 0.8665 (t0) cc_final: 0.8424 (t0) REVERT: C 499 ASP cc_start: 0.8330 (t0) cc_final: 0.8087 (t0) REVERT: C 570 ASP cc_start: 0.8278 (p0) cc_final: 0.7841 (p0) REVERT: C 596 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7798 (mp0) outliers start: 34 outliers final: 9 residues processed: 131 average time/residue: 1.3665 time to fit residues: 188.0640 Evaluate side-chains 101 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 251 ILE Chi-restraints excluded: chain B residue 296 ILE 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 B residue 597 GLN Chi-restraints excluded: chain C residue 177 LYS 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 1 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3555 r_free = 0.3555 target = 0.098076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.077958 restraints weight = 13303.175| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.05 r_work: 0.3049 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7475 Z= 0.155 Angle : 0.562 7.598 10126 Z= 0.294 Chirality : 0.045 0.157 1109 Planarity : 0.004 0.056 1277 Dihedral : 6.553 39.368 1194 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.64 % Allowed : 19.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 902 helix: 1.92 (0.34), residues: 242 sheet: 0.03 (0.33), residues: 241 loop : -0.52 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 351 HIS 0.005 0.001 HIS B 457 PHE 0.013 0.001 PHE B 482 TYR 0.010 0.001 TYR B 476 ARG 0.007 0.001 ARG C 201 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 305) hydrogen bonds : angle 5.51866 ( 930) covalent geometry : bond 0.00359 ( 7475) covalent geometry : angle 0.56197 (10126) *********************** 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 119 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8824 (ptpp) cc_final: 0.8349 (ttpp) REVERT: B 141 THR cc_start: 0.8983 (m) cc_final: 0.8749 (p) REVERT: B 167 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8050 (mm-30) REVERT: B 242 MET cc_start: 0.8573 (ttt) cc_final: 0.7983 (ttt) REVERT: B 401 GLU cc_start: 0.8224 (tp30) cc_final: 0.7850 (tm-30) REVERT: B 499 ASP cc_start: 0.8461 (t0) cc_final: 0.8088 (t0) REVERT: B 604 VAL cc_start: 0.8866 (m) cc_final: 0.8642 (p) REVERT: C 186 ASN cc_start: 0.8992 (m-40) cc_final: 0.8761 (t0) REVERT: C 237 ASP cc_start: 0.8699 (t70) cc_final: 0.8443 (t0) REVERT: C 271 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7471 (p0) REVERT: C 340 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7396 (mpp) REVERT: C 385 ASP cc_start: 0.8745 (t0) cc_final: 0.8382 (t0) REVERT: C 499 ASP cc_start: 0.8263 (t0) cc_final: 0.8040 (t0) REVERT: C 570 ASP cc_start: 0.8260 (p0) cc_final: 0.7857 (p0) REVERT: C 596 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7697 (mp0) outliers start: 20 outliers final: 10 residues processed: 114 average time/residue: 1.2124 time to fit residues: 146.1169 Evaluate side-chains 100 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 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 271 ASP 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 19 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 597 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 = 0.3508 r_free = 0.3508 target = 0.094927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074593 restraints weight = 13600.606| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.08 r_work: 0.2997 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 7475 Z= 0.265 Angle : 0.615 7.040 10126 Z= 0.322 Chirality : 0.047 0.163 1109 Planarity : 0.005 0.062 1277 Dihedral : 7.006 41.952 1194 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.70 % Allowed : 18.76 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.28), residues: 902 helix: 1.75 (0.34), residues: 244 sheet: -0.20 (0.32), residues: 249 loop : -0.65 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 351 HIS 0.008 0.001 HIS B 457 PHE 0.016 0.002 PHE B 482 TYR 0.021 0.002 TYR C 567 ARG 0.006 0.001 ARG C 201 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 305) hydrogen bonds : angle 5.61095 ( 930) covalent geometry : bond 0.00620 ( 7475) covalent geometry : angle 0.61524 (10126) *********************** 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 117 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8786 (ptpp) cc_final: 0.8235 (ttpp) REVERT: F 5 ARG cc_start: 0.8135 (ttp-170) cc_final: 0.7386 (ttp80) REVERT: B 239 ARG cc_start: 0.8677 (mtm-85) cc_final: 0.8432 (mpp-170) REVERT: B 242 MET cc_start: 0.8485 (ttt) cc_final: 0.8271 (ttm) REVERT: B 401 GLU cc_start: 0.8305 (tp30) cc_final: 0.7883 (tm-30) REVERT: B 499 ASP cc_start: 0.8565 (t0) cc_final: 0.8171 (t0) REVERT: B 571 LYS cc_start: 0.8899 (mttp) cc_final: 0.8252 (mtpm) REVERT: C 177 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8236 (ttmt) REVERT: C 186 ASN cc_start: 0.9087 (m-40) cc_final: 0.8816 (t0) REVERT: C 271 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7579 (p0) REVERT: C 272 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6509 (ptt-90) REVERT: C 370 GLN cc_start: 0.8261 (tt0) cc_final: 0.7979 (tt0) REVERT: C 385 ASP cc_start: 0.8814 (t0) cc_final: 0.8439 (t0) REVERT: C 596 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7707 (mp0) outliers start: 28 outliers final: 11 residues processed: 110 average time/residue: 1.5551 time to fit residues: 179.8931 Evaluate side-chains 103 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 470 THR Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 272 ARG 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 61 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 235 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 = 0.3534 r_free = 0.3534 target = 0.096751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.076669 restraints weight = 13298.028| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.04 r_work: 0.3033 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7475 Z= 0.179 Angle : 0.568 6.958 10126 Z= 0.299 Chirality : 0.046 0.162 1109 Planarity : 0.004 0.059 1277 Dihedral : 6.660 40.584 1194 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.30 % Allowed : 19.29 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.28), residues: 902 helix: 1.86 (0.34), residues: 243 sheet: -0.16 (0.32), residues: 245 loop : -0.60 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 351 HIS 0.006 0.001 HIS B 457 PHE 0.015 0.001 PHE B 482 TYR 0.014 0.001 TYR C 567 ARG 0.006 0.000 ARG C 201 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 305) hydrogen bonds : angle 5.39192 ( 930) covalent geometry : bond 0.00416 ( 7475) covalent geometry : angle 0.56793 (10126) *********************** 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 123 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8813 (ptpp) cc_final: 0.8246 (ttpp) REVERT: F 5 ARG cc_start: 0.8097 (ttp-170) cc_final: 0.7303 (ttp80) REVERT: B 141 THR cc_start: 0.9013 (m) cc_final: 0.8795 (p) REVERT: B 167 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 239 ARG cc_start: 0.8715 (mtm-85) cc_final: 0.8482 (mpp-170) REVERT: B 242 MET cc_start: 0.8453 (ttt) cc_final: 0.8226 (ttm) REVERT: B 401 GLU cc_start: 0.8308 (tp30) cc_final: 0.7914 (tm-30) REVERT: B 499 ASP cc_start: 0.8541 (t0) cc_final: 0.8094 (t0) REVERT: B 571 LYS cc_start: 0.8819 (mttp) cc_final: 0.8189 (mtpm) REVERT: C 186 ASN cc_start: 0.9084 (m-40) cc_final: 0.8828 (t0) REVERT: C 237 ASP cc_start: 0.8762 (t0) cc_final: 0.8431 (t0) REVERT: C 271 ASP cc_start: 0.7815 (p0) cc_final: 0.7610 (p0) REVERT: C 272 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6516 (ptt-90) REVERT: C 370 GLN cc_start: 0.8262 (tt0) cc_final: 0.7966 (tt0) REVERT: C 385 ASP cc_start: 0.8807 (t0) cc_final: 0.8402 (t0) REVERT: C 596 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7823 (mp0) outliers start: 25 outliers final: 11 residues processed: 117 average time/residue: 1.6909 time to fit residues: 209.3992 Evaluate side-chains 98 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 470 THR Chi-restraints excluded: chain C residue 272 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 56 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 235 GLN B 597 GLN C 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.095805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.076032 restraints weight = 13430.825| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.04 r_work: 0.3021 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 7475 Z= 0.207 Angle : 0.586 7.036 10126 Z= 0.306 Chirality : 0.046 0.166 1109 Planarity : 0.004 0.061 1277 Dihedral : 6.755 40.729 1194 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.30 % Allowed : 20.61 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.29), residues: 902 helix: 1.81 (0.34), residues: 243 sheet: -0.21 (0.32), residues: 249 loop : -0.67 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 351 HIS 0.006 0.001 HIS B 457 PHE 0.014 0.001 PHE B 482 TYR 0.018 0.002 TYR C 567 ARG 0.005 0.000 ARG C 201 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 305) hydrogen bonds : angle 5.37700 ( 930) covalent geometry : bond 0.00489 ( 7475) covalent geometry : angle 0.58626 (10126) *********************** 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 117 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8770 (ptpp) cc_final: 0.8114 (ttpp) REVERT: F 5 ARG cc_start: 0.8125 (ttp-170) cc_final: 0.7313 (ttp80) REVERT: B 167 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8100 (mm-30) REVERT: B 242 MET cc_start: 0.8448 (ttt) cc_final: 0.7969 (ttt) REVERT: B 336 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: B 388 LYS cc_start: 0.8776 (tppt) cc_final: 0.8537 (tppp) REVERT: B 401 GLU cc_start: 0.8308 (tp30) cc_final: 0.7946 (tm-30) REVERT: B 499 ASP cc_start: 0.8549 (t0) cc_final: 0.8079 (t0) REVERT: C 186 ASN cc_start: 0.9078 (m-40) cc_final: 0.8826 (t0) REVERT: C 201 ARG cc_start: 0.7896 (ttt-90) cc_final: 0.7671 (ttt-90) REVERT: C 237 ASP cc_start: 0.8763 (t0) cc_final: 0.8405 (t0) REVERT: C 271 ASP cc_start: 0.7863 (p0) cc_final: 0.7656 (p0) REVERT: C 272 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6542 (ptt-90) REVERT: C 370 GLN cc_start: 0.8232 (tt0) cc_final: 0.7949 (tt0) REVERT: C 385 ASP cc_start: 0.8843 (t0) cc_final: 0.8453 (t0) REVERT: C 596 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7837 (mp0) outliers start: 25 outliers final: 13 residues processed: 113 average time/residue: 1.3758 time to fit residues: 164.3787 Evaluate side-chains 104 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 266 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 597 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 = 0.3521 r_free = 0.3521 target = 0.095531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.075840 restraints weight = 13552.003| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.07 r_work: 0.3017 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 7475 Z= 0.214 Angle : 0.599 7.220 10126 Z= 0.314 Chirality : 0.046 0.174 1109 Planarity : 0.004 0.061 1277 Dihedral : 6.740 40.965 1194 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.30 % Allowed : 20.87 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.29), residues: 902 helix: 1.75 (0.34), residues: 244 sheet: -0.19 (0.32), residues: 249 loop : -0.69 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 351 HIS 0.006 0.001 HIS B 457 PHE 0.014 0.001 PHE B 482 TYR 0.017 0.001 TYR C 567 ARG 0.004 0.000 ARG C 201 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 305) hydrogen bonds : angle 5.39309 ( 930) covalent geometry : bond 0.00504 ( 7475) covalent geometry : angle 0.59929 (10126) *********************** 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 116 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8778 (ptpp) cc_final: 0.8106 (ttpp) REVERT: F 5 ARG cc_start: 0.8126 (ttp-170) cc_final: 0.7317 (ttp80) REVERT: B 167 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8099 (mm-30) REVERT: B 242 MET cc_start: 0.8443 (ttt) cc_final: 0.7977 (ttt) REVERT: B 299 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8388 (mt-10) REVERT: B 336 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: B 401 GLU cc_start: 0.8313 (tp30) cc_final: 0.7958 (tm-30) REVERT: B 499 ASP cc_start: 0.8549 (t0) cc_final: 0.8072 (t0) REVERT: C 186 ASN cc_start: 0.9091 (m-40) cc_final: 0.8841 (t0) REVERT: C 201 ARG cc_start: 0.7894 (ttt-90) cc_final: 0.7660 (ttt-90) REVERT: C 237 ASP cc_start: 0.8771 (t0) cc_final: 0.8376 (t0) REVERT: C 271 ASP cc_start: 0.7890 (p0) cc_final: 0.7681 (p0) REVERT: C 272 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6570 (ptt-90) REVERT: C 340 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7451 (mpp) REVERT: C 370 GLN cc_start: 0.8241 (tt0) cc_final: 0.7958 (tt0) REVERT: C 385 ASP cc_start: 0.8856 (t0) cc_final: 0.8457 (t0) REVERT: C 596 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7843 (mp0) outliers start: 25 outliers final: 13 residues processed: 112 average time/residue: 1.7731 time to fit residues: 210.7164 Evaluate side-chains 103 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 336 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 295 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 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 = 0.3558 r_free = 0.3558 target = 0.098542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079274 restraints weight = 13862.947| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.05 r_work: 0.3169 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7475 Z= 0.128 Angle : 0.575 8.111 10126 Z= 0.299 Chirality : 0.046 0.182 1109 Planarity : 0.004 0.059 1277 Dihedral : 6.368 39.959 1194 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.51 % Allowed : 22.59 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.29), residues: 902 helix: 1.93 (0.35), residues: 242 sheet: -0.04 (0.32), residues: 245 loop : -0.61 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 180 HIS 0.004 0.001 HIS B 457 PHE 0.025 0.001 PHE C 181 TYR 0.012 0.001 TYR F 3 ARG 0.007 0.000 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 305) hydrogen bonds : angle 5.15946 ( 930) covalent geometry : bond 0.00294 ( 7475) covalent geometry : angle 0.57546 (10126) *********************** 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 118 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8858 (ptpp) cc_final: 0.8233 (ttpp) REVERT: B 167 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8097 (mm-30) REVERT: B 194 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7922 (tmtt) REVERT: B 242 MET cc_start: 0.8464 (ttt) cc_final: 0.8037 (ttt) REVERT: B 299 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8425 (mt-10) REVERT: B 336 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: B 388 LYS cc_start: 0.8753 (tppt) cc_final: 0.8547 (tppp) REVERT: B 401 GLU cc_start: 0.8292 (tp30) cc_final: 0.7931 (pp20) REVERT: B 499 ASP cc_start: 0.8558 (t0) cc_final: 0.8153 (t0) REVERT: B 571 LYS cc_start: 0.8743 (mttp) cc_final: 0.8244 (ttpp) REVERT: C 186 ASN cc_start: 0.9097 (m-40) cc_final: 0.8866 (t0) REVERT: C 237 ASP cc_start: 0.8747 (t0) cc_final: 0.8455 (t0) REVERT: C 272 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6667 (ptt-90) REVERT: C 319 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8033 (mm) REVERT: C 370 GLN cc_start: 0.8210 (tt0) cc_final: 0.7900 (tt0) REVERT: C 385 ASP cc_start: 0.8775 (t0) cc_final: 0.8412 (t0) REVERT: C 596 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7842 (mp0) outliers start: 19 outliers final: 10 residues processed: 115 average time/residue: 2.4868 time to fit residues: 304.1971 Evaluate side-chains 100 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 C residue 266 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 319 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 235 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 = 0.3548 r_free = 0.3548 target = 0.097975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.078622 restraints weight = 13917.525| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.07 r_work: 0.3151 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7475 Z= 0.144 Angle : 0.601 9.170 10126 Z= 0.314 Chirality : 0.046 0.187 1109 Planarity : 0.004 0.060 1277 Dihedral : 6.429 40.521 1194 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.38 % Allowed : 22.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.29), residues: 902 helix: 1.81 (0.35), residues: 243 sheet: 0.04 (0.33), residues: 245 loop : -0.60 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 180 HIS 0.005 0.001 HIS B 457 PHE 0.013 0.001 PHE B 482 TYR 0.027 0.001 TYR C 567 ARG 0.011 0.000 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 305) hydrogen bonds : angle 5.23732 ( 930) covalent geometry : bond 0.00339 ( 7475) covalent geometry : angle 0.60132 (10126) *********************** 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 104 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8873 (ptpp) cc_final: 0.8245 (ttpp) REVERT: B 167 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8068 (mm-30) REVERT: B 242 MET cc_start: 0.8499 (ttt) cc_final: 0.8078 (ttt) REVERT: B 336 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: B 401 GLU cc_start: 0.8326 (tp30) cc_final: 0.7974 (pp20) REVERT: B 481 MET cc_start: 0.8624 (ppp) cc_final: 0.8422 (ppp) REVERT: B 499 ASP cc_start: 0.8559 (t0) cc_final: 0.8176 (t0) REVERT: C 186 ASN cc_start: 0.9093 (m-40) cc_final: 0.8830 (t0) REVERT: C 237 ASP cc_start: 0.8761 (t0) cc_final: 0.8477 (t0) REVERT: C 272 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6739 (ptt-90) REVERT: C 370 GLN cc_start: 0.8230 (tt0) cc_final: 0.7905 (tt0) REVERT: C 385 ASP cc_start: 0.8763 (t0) cc_final: 0.8428 (t0) REVERT: C 596 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7882 (mp0) outliers start: 18 outliers final: 9 residues processed: 99 average time/residue: 1.3957 time to fit residues: 145.7832 Evaluate side-chains 97 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 300 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 272 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 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 = 0.3515 r_free = 0.3515 target = 0.096709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.076715 restraints weight = 13859.709| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.10 r_work: 0.3030 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7475 Z= 0.173 Angle : 0.619 9.550 10126 Z= 0.320 Chirality : 0.046 0.208 1109 Planarity : 0.004 0.061 1277 Dihedral : 6.571 40.658 1194 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.72 % Allowed : 23.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.29), residues: 902 helix: 1.76 (0.35), residues: 244 sheet: 0.01 (0.33), residues: 240 loop : -0.62 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 180 HIS 0.006 0.001 HIS B 457 PHE 0.022 0.001 PHE C 181 TYR 0.034 0.002 TYR C 567 ARG 0.011 0.000 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 305) hydrogen bonds : angle 5.32062 ( 930) covalent geometry : bond 0.00410 ( 7475) covalent geometry : angle 0.61852 (10126) ********************** 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 101 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8213 (ttm170) cc_final: 0.8011 (ttp80) REVERT: A 9 LYS cc_start: 0.8847 (ptpp) cc_final: 0.8199 (ttpp) REVERT: B 167 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8111 (mm-30) REVERT: B 242 MET cc_start: 0.8416 (ttt) cc_final: 0.7980 (ttt) REVERT: B 336 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: B 401 GLU cc_start: 0.8291 (tp30) cc_final: 0.7911 (pp20) REVERT: B 499 ASP cc_start: 0.8539 (t0) cc_final: 0.8149 (t0) REVERT: B 571 LYS cc_start: 0.8782 (mttp) cc_final: 0.8315 (ttpp) REVERT: C 186 ASN cc_start: 0.9095 (m-40) cc_final: 0.8810 (t0) REVERT: C 237 ASP cc_start: 0.8765 (t0) cc_final: 0.8425 (t0) REVERT: C 272 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6736 (ptt-90) REVERT: C 370 GLN cc_start: 0.8249 (tt0) cc_final: 0.7939 (tt0) REVERT: C 385 ASP cc_start: 0.8786 (t0) cc_final: 0.8426 (t0) REVERT: C 596 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7799 (mp0) outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 1.2770 time to fit residues: 134.8301 Evaluate side-chains 99 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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 266 SER Chi-restraints excluded: chain C residue 272 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 64 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 0.0060 chunk 69 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 86 optimal weight: 0.0870 overall best weight: 0.4974 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.099807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.079913 restraints weight = 13437.937| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.08 r_work: 0.3091 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7475 Z= 0.119 Angle : 0.601 9.446 10126 Z= 0.310 Chirality : 0.045 0.171 1109 Planarity : 0.004 0.059 1277 Dihedral : 6.290 40.919 1194 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.32 % Allowed : 23.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.29), residues: 902 helix: 1.81 (0.35), residues: 243 sheet: 0.04 (0.34), residues: 234 loop : -0.51 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 180 HIS 0.003 0.001 HIS B 457 PHE 0.012 0.001 PHE B 482 TYR 0.025 0.001 TYR C 567 ARG 0.010 0.000 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 305) hydrogen bonds : angle 5.16808 ( 930) covalent geometry : bond 0.00276 ( 7475) covalent geometry : angle 0.60114 (10126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6932.48 seconds wall clock time: 125 minutes 1.78 seconds (7501.78 seconds total)