Starting phenix.real_space_refine on Sun Apr 5 21:29:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10tu_75467/04_2026/10tu_75467_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/10tu_75467/04_2026/10tu_75467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10tu_75467/04_2026/10tu_75467_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10tu_75467/04_2026/10tu_75467_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10tu_75467/04_2026/10tu_75467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10tu_75467/04_2026/10tu_75467.map" } resolution = 3.2 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= 0.009 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: 6 Type Number sf(0) Gaussians As 2 7.32 5 S 20 5.16 5 C 4266 2.51 5 N 1046 2.21 5 O 1076 1.98 5 H 6788 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13198 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6595 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 412} Chain: "B" Number of atoms: 6595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6595 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 412} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'TAS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'TAS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.08, per 1000 atoms: 0.16 Number of scatterers: 13198 At special positions: 0 Unit cell: (111.15, 86.45, 73.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) As 2 32.98 S 20 16.00 O 1076 8.00 N 1046 7.00 C 4266 6.00 H 6788 1.00 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: 1.26 Conformation dependent library (CDL) restraints added in 481.7 milliseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 92.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 Processing helix chain 'A' and resid 19 through 22 Processing helix chain 'A' and resid 23 through 38 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 73 removed outlier: 3.546A pdb=" N VAL A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASN A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 90 through 115 removed outlier: 7.854A pdb=" N ASN A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ASP A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 removed outlier: 4.025A pdb=" N ILE A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 150 removed outlier: 4.184A pdb=" N ASP A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 158 through 168 Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'A' and resid 180 through 198 Processing helix chain 'A' and resid 199 through 202 removed outlier: 3.510A pdb=" N ILE A 202 " --> pdb=" O ARG A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 202' Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.541A pdb=" N GLN A 210 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.519A pdb=" N ILE A 218 " --> pdb=" O ASN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 245 removed outlier: 3.792A pdb=" N ILE A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Proline residue: A 243 - end of helix Processing helix chain 'A' and resid 247 through 266 removed outlier: 3.573A pdb=" N VAL A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 281 through 299 removed outlier: 3.592A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 removed outlier: 4.015A pdb=" N LEU A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 336 Processing helix chain 'A' and resid 336 through 350 removed outlier: 3.862A pdb=" N THR A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 342 " --> pdb=" O MET A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 372 Processing helix chain 'A' and resid 373 through 379 Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 380 through 393 Processing helix chain 'A' and resid 398 through 427 Proline residue: A 412 - end of helix Processing helix chain 'B' and resid 2 through 18 Processing helix chain 'B' and resid 19 through 22 Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 45 through 73 removed outlier: 3.546A pdb=" N VAL B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASN B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA B 56 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 90 through 115 removed outlier: 7.854A pdb=" N ASN B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ASP B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 4.025A pdb=" N ILE B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 150 removed outlier: 4.184A pdb=" N ASP B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 180 through 198 Processing helix chain 'B' and resid 199 through 202 removed outlier: 3.509A pdb=" N ILE B 202 " --> pdb=" O ARG B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 202' Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.542A pdb=" N GLN B 210 " --> pdb=" O ASP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 removed outlier: 3.519A pdb=" N ILE B 218 " --> pdb=" O ASN B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 245 removed outlier: 3.792A pdb=" N ILE B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU B 242 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 247 through 266 removed outlier: 3.572A pdb=" N VAL B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 281 through 299 removed outlier: 3.592A pdb=" N LEU B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 297 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 314 removed outlier: 4.014A pdb=" N LEU B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 336 Processing helix chain 'B' and resid 336 through 350 removed outlier: 3.862A pdb=" N THR B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 372 Processing helix chain 'B' and resid 373 through 379 Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 380 through 393 Processing helix chain 'B' and resid 398 through 427 Proline residue: B 412 - end of helix 529 hydrogen bonds defined for protein. 1551 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: 2.68 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6708 1.03 - 1.22: 80 1.22 - 1.41: 2621 1.41 - 1.61: 3887 1.61 - 1.80: 46 Bond restraints: 13342 Sorted by residual: bond pdb=" N VAL A 292 " pdb=" H VAL A 292 " ideal model delta sigma weight residual 0.860 1.038 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" N VAL B 292 " pdb=" H VAL B 292 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N LEU B 296 " pdb=" H LEU B 296 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" N GLY B 295 " pdb=" H GLY B 295 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" N LEU A 296 " pdb=" H LEU A 296 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.72e+01 ... (remaining 13337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 24250 3.64 - 7.29: 28 7.29 - 10.93: 2 10.93 - 14.57: 2 14.57 - 18.22: 2 Bond angle restraints: 24284 Sorted by residual: angle pdb=" O1 TAS B 501 " pdb="AS TAS B 501 " pdb=" O2 TAS B 501 " ideal model delta sigma weight residual 91.74 109.96 -18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" O1 TAS A 501 " pdb="AS TAS A 501 " pdb=" O2 TAS A 501 " ideal model delta sigma weight residual 91.74 109.95 -18.21 3.00e+00 1.11e-01 3.68e+01 angle pdb=" O1 TAS A 501 " pdb="AS TAS A 501 " pdb=" O3 TAS A 501 " ideal model delta sigma weight residual 95.76 109.11 -13.35 3.00e+00 1.11e-01 1.98e+01 angle pdb=" O1 TAS B 501 " pdb="AS TAS B 501 " pdb=" O3 TAS B 501 " ideal model delta sigma weight residual 95.76 109.06 -13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" N TYR A 294 " pdb=" CA TYR A 294 " pdb=" C TYR A 294 " ideal model delta sigma weight residual 112.89 108.00 4.89 1.24e+00 6.50e-01 1.55e+01 ... (remaining 24279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 5557 16.45 - 32.90: 444 32.90 - 49.35: 111 49.35 - 65.79: 74 65.79 - 82.24: 2 Dihedral angle restraints: 6188 sinusoidal: 3296 harmonic: 2892 Sorted by residual: dihedral pdb=" CA LEU A 152 " pdb=" C LEU A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta harmonic sigma weight residual -180.00 -160.35 -19.65 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N PRO B 153 " pdb=" CA PRO B 153 " ideal model delta harmonic sigma weight residual -180.00 -160.35 -19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ILE B 52 " pdb=" C ILE B 52 " pdb=" N VAL B 53 " pdb=" CA VAL B 53 " ideal model delta harmonic sigma weight residual 180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 6185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 659 0.035 - 0.070: 337 0.070 - 0.105: 110 0.105 - 0.141: 18 0.141 - 0.176: 4 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CA VAL B 293 " pdb=" N VAL B 293 " pdb=" C VAL B 293 " pdb=" CB VAL B 293 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA VAL A 293 " pdb=" N VAL A 293 " pdb=" C VAL A 293 " pdb=" CB VAL A 293 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA VAL A 292 " pdb=" N VAL A 292 " pdb=" C VAL A 292 " pdb=" CB VAL A 292 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 1125 not shown) Planarity restraints: 1906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 296 " -0.013 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" N ARG A 297 " 0.043 2.00e-02 2.50e+03 pdb=" CA ARG A 297 " -0.011 2.00e-02 2.50e+03 pdb=" H ARG A 297 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 296 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" N ARG B 297 " -0.040 2.00e-02 2.50e+03 pdb=" CA ARG B 297 " 0.010 2.00e-02 2.50e+03 pdb=" H ARG B 297 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 50 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C TRP A 50 " -0.032 2.00e-02 2.50e+03 pdb=" O TRP A 50 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 51 " 0.011 2.00e-02 2.50e+03 ... (remaining 1903 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.41: 6189 2.41 - 2.98: 32501 2.98 - 3.56: 39198 3.56 - 4.13: 50153 4.13 - 4.70: 81190 Nonbonded interactions: 209231 Sorted by model distance: nonbonded pdb=" HE ARG A 20 " pdb="HH21 ARG B 272 " model vdw 1.840 2.100 nonbonded pdb="HH21 ARG A 272 " pdb=" HE ARG B 20 " model vdw 1.858 2.100 nonbonded pdb="HH21 ARG A 20 " pdb=" HE ARG B 272 " model vdw 1.905 2.100 nonbonded pdb=" HD2 ARG A 424 " pdb="HH11 ARG A 424 " model vdw 1.909 2.270 nonbonded pdb=" HD2 ARG B 424 " pdb="HH11 ARG B 424 " model vdw 1.910 2.270 ... (remaining 209226 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.110 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: 0.080 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.000 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.008 0.072 6554 Z= 0.321 Angle : 0.731 18.218 8972 Z= 0.382 Chirality : 0.045 0.176 1128 Planarity : 0.006 0.036 1082 Dihedral : 11.078 82.242 2196 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.24), residues: 852 helix: -1.50 (0.14), residues: 698 sheet: None (None), residues: 0 loop : 1.90 (0.57), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 85 TYR 0.017 0.002 TYR A 175 PHE 0.017 0.002 PHE A 109 TRP 0.013 0.001 TRP A 386 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00791 ( 6554) covalent geometry : angle 0.73105 ( 8972) hydrogen bonds : bond 0.13283 ( 529) hydrogen bonds : angle 6.15461 ( 1551) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.8087 (t60) cc_final: 0.7196 (t60) REVERT: A 88 LYS cc_start: 0.8383 (ptpt) cc_final: 0.8148 (ptpp) REVERT: A 388 HIS cc_start: 0.7468 (m90) cc_final: 0.7025 (m-70) REVERT: B 17 TRP cc_start: 0.8030 (t60) cc_final: 0.7170 (t60) REVERT: B 88 LYS cc_start: 0.8415 (ptpt) cc_final: 0.8169 (ptpp) REVERT: B 388 HIS cc_start: 0.7483 (m90) cc_final: 0.7056 (m-70) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2325 time to fit residues: 27.8633 Evaluate side-chains 67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.160340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142081 restraints weight = 22167.397| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.99 r_work: 0.3539 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6554 Z= 0.157 Angle : 0.542 5.013 8972 Z= 0.293 Chirality : 0.036 0.139 1128 Planarity : 0.005 0.036 1082 Dihedral : 3.838 20.962 900 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.61 % Allowed : 2.74 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.28), residues: 852 helix: 0.49 (0.18), residues: 706 sheet: None (None), residues: 0 loop : 1.54 (0.59), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 200 TYR 0.007 0.001 TYR A 175 PHE 0.007 0.001 PHE A 145 TRP 0.010 0.001 TRP A 386 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6554) covalent geometry : angle 0.54168 ( 8972) hydrogen bonds : bond 0.05108 ( 529) hydrogen bonds : angle 4.65527 ( 1551) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.8153 (t60) cc_final: 0.7344 (t60) REVERT: A 72 GLU cc_start: 0.7933 (mp0) cc_final: 0.7693 (mp0) REVERT: A 220 ASP cc_start: 0.7590 (t0) cc_final: 0.7093 (t0) REVERT: A 335 MET cc_start: 0.8526 (ptm) cc_final: 0.8272 (ptt) REVERT: B 17 TRP cc_start: 0.8116 (t60) cc_final: 0.7316 (t60) REVERT: B 72 GLU cc_start: 0.7919 (mp0) cc_final: 0.7677 (mp0) REVERT: B 220 ASP cc_start: 0.7606 (t0) cc_final: 0.7105 (t0) outliers start: 4 outliers final: 4 residues processed: 82 average time/residue: 0.1481 time to fit residues: 17.4019 Evaluate side-chains 77 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.159385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140727 restraints weight = 22675.170| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.05 r_work: 0.3518 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6554 Z= 0.141 Angle : 0.496 4.208 8972 Z= 0.267 Chirality : 0.036 0.161 1128 Planarity : 0.004 0.035 1082 Dihedral : 3.690 20.139 900 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.22 % Allowed : 3.80 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.28), residues: 852 helix: 1.08 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 0.88 (0.56), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 85 TYR 0.006 0.001 TYR A 175 PHE 0.007 0.001 PHE A 95 TRP 0.009 0.001 TRP B 386 HIS 0.002 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6554) covalent geometry : angle 0.49580 ( 8972) hydrogen bonds : bond 0.04713 ( 529) hydrogen bonds : angle 4.38550 ( 1551) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.8131 (t60) cc_final: 0.7357 (t60) REVERT: A 72 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: A 220 ASP cc_start: 0.7751 (t0) cc_final: 0.7279 (t0) REVERT: A 335 MET cc_start: 0.8559 (ptm) cc_final: 0.8315 (ptt) REVERT: B 17 TRP cc_start: 0.8127 (t60) cc_final: 0.7368 (t60) REVERT: B 72 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: B 220 ASP cc_start: 0.7755 (t0) cc_final: 0.7297 (t0) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.1325 time to fit residues: 15.3605 Evaluate side-chains 85 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130933 restraints weight = 21671.743| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.82 r_work: 0.3141 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6554 Z= 0.162 Angle : 0.497 4.367 8972 Z= 0.267 Chirality : 0.036 0.136 1128 Planarity : 0.004 0.035 1082 Dihedral : 3.680 19.557 900 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.52 % Allowed : 4.26 % Favored : 94.22 % 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 are not related in a simple way. whole: 1.67 (0.29), residues: 852 helix: 1.30 (0.19), residues: 700 sheet: None (None), residues: 0 loop : 0.61 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 85 TYR 0.012 0.001 TYR B 206 PHE 0.008 0.001 PHE A 145 TRP 0.008 0.001 TRP B 386 HIS 0.002 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6554) covalent geometry : angle 0.49669 ( 8972) hydrogen bonds : bond 0.04619 ( 529) hydrogen bonds : angle 4.25105 ( 1551) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.7984 (t60) cc_final: 0.7148 (t60) REVERT: A 72 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: A 220 ASP cc_start: 0.7687 (t0) cc_final: 0.7151 (t0) REVERT: A 335 MET cc_start: 0.8488 (ptm) cc_final: 0.8249 (ptt) REVERT: B 17 TRP cc_start: 0.7959 (t60) cc_final: 0.7138 (t60) REVERT: B 72 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: B 220 ASP cc_start: 0.7702 (t0) cc_final: 0.7189 (t0) outliers start: 10 outliers final: 7 residues processed: 84 average time/residue: 0.1381 time to fit residues: 16.9807 Evaluate side-chains 90 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN B 51 GLN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.112279 restraints weight = 22138.060| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.93 r_work: 0.3205 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6554 Z= 0.136 Angle : 0.472 4.212 8972 Z= 0.255 Chirality : 0.036 0.145 1128 Planarity : 0.004 0.036 1082 Dihedral : 3.653 19.045 900 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.82 % Allowed : 5.47 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.29), residues: 852 helix: 1.48 (0.19), residues: 702 sheet: None (None), residues: 0 loop : 0.62 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 424 TYR 0.006 0.001 TYR B 363 PHE 0.007 0.001 PHE A 95 TRP 0.007 0.001 TRP B 386 HIS 0.001 0.000 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6554) covalent geometry : angle 0.47208 ( 8972) hydrogen bonds : bond 0.04367 ( 529) hydrogen bonds : angle 4.17405 ( 1551) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.8090 (t60) cc_final: 0.7268 (t60) REVERT: A 72 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 220 ASP cc_start: 0.7772 (t0) cc_final: 0.7340 (t0) REVERT: A 335 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8297 (ptt) REVERT: B 17 TRP cc_start: 0.8068 (t60) cc_final: 0.7257 (t60) REVERT: B 72 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: B 220 ASP cc_start: 0.7778 (t0) cc_final: 0.7346 (t0) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 0.1356 time to fit residues: 14.9565 Evaluate side-chains 85 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 161 ASN B 82 HIS B 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109507 restraints weight = 22287.324| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.88 r_work: 0.3171 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6554 Z= 0.168 Angle : 0.491 4.198 8972 Z= 0.265 Chirality : 0.036 0.136 1128 Planarity : 0.004 0.036 1082 Dihedral : 3.682 19.319 900 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.82 % Allowed : 6.99 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.28), residues: 852 helix: 1.48 (0.19), residues: 702 sheet: None (None), residues: 0 loop : 0.21 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 392 TYR 0.007 0.001 TYR B 363 PHE 0.009 0.001 PHE B 145 TRP 0.007 0.001 TRP B 386 HIS 0.002 0.000 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 6554) covalent geometry : angle 0.49138 ( 8972) hydrogen bonds : bond 0.04573 ( 529) hydrogen bonds : angle 4.16365 ( 1551) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.8137 (t60) cc_final: 0.7313 (t60) REVERT: A 72 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: A 196 PHE cc_start: 0.8083 (t80) cc_final: 0.7847 (t80) REVERT: A 220 ASP cc_start: 0.7864 (t0) cc_final: 0.7431 (t0) REVERT: A 335 MET cc_start: 0.8540 (ptm) cc_final: 0.8318 (ptt) REVERT: B 17 TRP cc_start: 0.8081 (t60) cc_final: 0.7300 (t60) REVERT: B 72 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: B 220 ASP cc_start: 0.7858 (t0) cc_final: 0.7432 (t0) outliers start: 12 outliers final: 6 residues processed: 81 average time/residue: 0.1375 time to fit residues: 16.3191 Evaluate side-chains 86 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 314 GLN B 51 GLN B 314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.110837 restraints weight = 22275.108| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.82 r_work: 0.3194 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6554 Z= 0.133 Angle : 0.467 4.192 8972 Z= 0.253 Chirality : 0.035 0.134 1128 Planarity : 0.004 0.035 1082 Dihedral : 3.626 18.802 900 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.22 % Allowed : 7.29 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.28), residues: 852 helix: 1.81 (0.20), residues: 688 sheet: None (None), residues: 0 loop : 0.13 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 424 TYR 0.007 0.001 TYR A 175 PHE 0.014 0.001 PHE B 196 TRP 0.007 0.001 TRP A 386 HIS 0.001 0.000 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6554) covalent geometry : angle 0.46659 ( 8972) hydrogen bonds : bond 0.04288 ( 529) hydrogen bonds : angle 4.09128 ( 1551) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.8100 (t60) cc_final: 0.7274 (t60) REVERT: A 72 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: A 196 PHE cc_start: 0.8062 (t80) cc_final: 0.7819 (t80) REVERT: A 220 ASP cc_start: 0.7792 (t0) cc_final: 0.7364 (t0) REVERT: A 335 MET cc_start: 0.8418 (ptm) cc_final: 0.8208 (ptt) REVERT: B 17 TRP cc_start: 0.8067 (t60) cc_final: 0.7260 (t60) REVERT: B 72 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: B 220 ASP cc_start: 0.7770 (t0) cc_final: 0.7361 (t0) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.1257 time to fit residues: 15.3149 Evaluate side-chains 87 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.0050 chunk 79 optimal weight: 0.0370 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126016 restraints weight = 21849.543| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.73 r_work: 0.3242 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6554 Z= 0.123 Angle : 0.453 4.074 8972 Z= 0.242 Chirality : 0.035 0.134 1128 Planarity : 0.004 0.034 1082 Dihedral : 3.568 18.663 900 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.22 % Allowed : 7.45 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.29), residues: 852 helix: 1.98 (0.20), residues: 688 sheet: None (None), residues: 0 loop : 0.16 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 424 TYR 0.007 0.001 TYR A 363 PHE 0.011 0.001 PHE B 196 TRP 0.007 0.001 TRP A 78 HIS 0.001 0.000 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6554) covalent geometry : angle 0.45327 ( 8972) hydrogen bonds : bond 0.04083 ( 529) hydrogen bonds : angle 4.00628 ( 1551) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.8130 (t60) cc_final: 0.7346 (t60) REVERT: A 72 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: A 196 PHE cc_start: 0.8044 (t80) cc_final: 0.7825 (t80) REVERT: A 220 ASP cc_start: 0.7771 (t0) cc_final: 0.7416 (t0) REVERT: A 335 MET cc_start: 0.8440 (ptm) cc_final: 0.8233 (ptt) REVERT: B 17 TRP cc_start: 0.8136 (t60) cc_final: 0.7350 (t60) REVERT: B 72 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: B 220 ASP cc_start: 0.7763 (t0) cc_final: 0.7409 (t0) outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 0.1209 time to fit residues: 15.0046 Evaluate side-chains 84 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 314 GLN B 51 GLN B 314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.128084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109117 restraints weight = 22497.895| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.89 r_work: 0.3146 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6554 Z= 0.176 Angle : 0.493 4.135 8972 Z= 0.264 Chirality : 0.036 0.134 1128 Planarity : 0.004 0.035 1082 Dihedral : 3.627 19.038 900 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.22 % Allowed : 7.75 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.28), residues: 852 helix: 1.82 (0.19), residues: 688 sheet: None (None), residues: 0 loop : -0.00 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 85 TYR 0.007 0.001 TYR A 363 PHE 0.011 0.001 PHE B 196 TRP 0.006 0.001 TRP A 386 HIS 0.002 0.000 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 6554) covalent geometry : angle 0.49250 ( 8972) hydrogen bonds : bond 0.04436 ( 529) hydrogen bonds : angle 4.07301 ( 1551) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 17 TRP cc_start: 0.8110 (t60) cc_final: 0.7307 (t60) REVERT: A 72 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: A 196 PHE cc_start: 0.8099 (t80) cc_final: 0.7867 (t80) REVERT: A 220 ASP cc_start: 0.7897 (t0) cc_final: 0.7449 (t0) REVERT: A 335 MET cc_start: 0.8459 (ptm) cc_final: 0.8257 (ptt) REVERT: A 349 ASP cc_start: 0.8018 (t70) cc_final: 0.7810 (t0) REVERT: B 17 TRP cc_start: 0.8123 (t60) cc_final: 0.7321 (t60) REVERT: B 72 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: B 220 ASP cc_start: 0.7871 (t0) cc_final: 0.7439 (t0) REVERT: B 349 ASP cc_start: 0.8011 (t70) cc_final: 0.7809 (t0) outliers start: 8 outliers final: 5 residues processed: 80 average time/residue: 0.1097 time to fit residues: 13.3477 Evaluate side-chains 79 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.109057 restraints weight = 22400.139| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.88 r_work: 0.3078 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6554 Z= 0.169 Angle : 0.487 4.136 8972 Z= 0.261 Chirality : 0.036 0.136 1128 Planarity : 0.004 0.036 1082 Dihedral : 3.637 19.429 900 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.22 % Allowed : 7.90 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.28), residues: 852 helix: 1.82 (0.19), residues: 688 sheet: None (None), residues: 0 loop : -0.15 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 424 TYR 0.006 0.001 TYR A 363 PHE 0.011 0.001 PHE B 196 TRP 0.007 0.001 TRP B 78 HIS 0.001 0.000 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6554) covalent geometry : angle 0.48726 ( 8972) hydrogen bonds : bond 0.04389 ( 529) hydrogen bonds : angle 4.07687 ( 1551) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.341 Fit side-chains REVERT: A 17 TRP cc_start: 0.8044 (t60) cc_final: 0.7227 (t60) REVERT: A 72 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 196 PHE cc_start: 0.8085 (t80) cc_final: 0.7832 (t80) REVERT: A 220 ASP cc_start: 0.7848 (t0) cc_final: 0.7352 (t0) REVERT: A 349 ASP cc_start: 0.7906 (t70) cc_final: 0.7691 (t0) REVERT: B 17 TRP cc_start: 0.8044 (t60) cc_final: 0.7231 (t60) REVERT: B 72 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: B 220 ASP cc_start: 0.7841 (t0) cc_final: 0.7349 (t0) REVERT: B 349 ASP cc_start: 0.7891 (t70) cc_final: 0.7674 (t0) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 0.1251 time to fit residues: 14.4797 Evaluate side-chains 79 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 314 GLN B 51 GLN B 314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126913 restraints weight = 21887.323| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.75 r_work: 0.3254 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6554 Z= 0.128 Angle : 0.466 4.148 8972 Z= 0.249 Chirality : 0.035 0.134 1128 Planarity : 0.004 0.035 1082 Dihedral : 3.606 18.994 900 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.06 % Allowed : 8.05 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.28), residues: 852 helix: 1.97 (0.19), residues: 688 sheet: None (None), residues: 0 loop : -0.03 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 424 TYR 0.006 0.001 TYR A 363 PHE 0.010 0.001 PHE B 196 TRP 0.006 0.001 TRP A 386 HIS 0.001 0.000 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6554) covalent geometry : angle 0.46617 ( 8972) hydrogen bonds : bond 0.04133 ( 529) hydrogen bonds : angle 4.00523 ( 1551) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3468.47 seconds wall clock time: 59 minutes 19.97 seconds (3559.97 seconds total)