Starting phenix.real_space_refine on Thu Feb 13 21:59:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d13_27114/02_2025/8d13_27114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d13_27114/02_2025/8d13_27114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d13_27114/02_2025/8d13_27114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d13_27114/02_2025/8d13_27114.map" model { file = "/net/cci-nas-00/data/ceres_data/8d13_27114/02_2025/8d13_27114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d13_27114/02_2025/8d13_27114.cif" } resolution = 2.43 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= 0.001 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 P 6 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 5541 2.51 5 N 1482 2.21 5 O 2121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9216 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 144 Classifications: {'water': 144} Link IDs: {None: 143} Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 144 Classifications: {'water': 144} Link IDs: {None: 143} Chain: "C" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 144 Classifications: {'water': 144} Link IDs: {None: 143} Time building chain proxies: 9.05, per 1000 atoms: 0.98 Number of scatterers: 9216 At special positions: 0 Unit cell: (90.64, 85.49, 140.08, 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) S 63 16.00 P 6 15.00 Mg 3 11.99 O 2121 8.00 N 1482 7.00 C 5541 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: 2.29 Conformation dependent library (CDL) restraints added in 974.8 milliseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 18 sheets defined 50.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.000A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.579A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.265A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.921A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.999A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.523A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.580A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.265A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.923A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.000A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.515A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.579A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.266A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.923A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.581A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.431A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.580A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.430A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.149A pdb=" N GLN C 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.581A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.430A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 454 hydrogen bonds defined for protein. 1152 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: 3.92 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1594 1.32 - 1.45: 2228 1.45 - 1.57: 5034 1.57 - 1.69: 9 1.69 - 1.81: 111 Bond restraints: 8976 Sorted by residual: bond pdb=" C LEU A 140 " pdb=" O LEU A 140 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.17e-02 7.31e+03 8.30e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.94e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.89e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.87e+00 bond pdb=" C LEU B 140 " pdb=" O LEU B 140 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.17e-02 7.31e+03 7.36e+00 ... (remaining 8971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 11978 1.98 - 3.95: 157 3.95 - 5.93: 33 5.93 - 7.91: 11 7.91 - 9.88: 4 Bond angle restraints: 12183 Sorted by residual: angle pdb=" N GLY A 182 " pdb=" CA GLY A 182 " pdb=" C GLY A 182 " ideal model delta sigma weight residual 112.83 121.09 -8.26 1.22e+00 6.72e-01 4.58e+01 angle pdb=" N GLY C 182 " pdb=" CA GLY C 182 " pdb=" C GLY C 182 " ideal model delta sigma weight residual 112.83 120.29 -7.46 1.22e+00 6.72e-01 3.73e+01 angle pdb=" N GLY B 182 " pdb=" CA GLY B 182 " pdb=" C GLY B 182 " ideal model delta sigma weight residual 112.83 119.99 -7.16 1.22e+00 6.72e-01 3.45e+01 angle pdb=" N GLN B 137 " pdb=" CA GLN B 137 " pdb=" C GLN B 137 " ideal model delta sigma weight residual 111.28 117.53 -6.25 1.09e+00 8.42e-01 3.28e+01 angle pdb=" N GLN A 137 " pdb=" CA GLN A 137 " pdb=" C GLN A 137 " ideal model delta sigma weight residual 111.28 117.09 -5.81 1.09e+00 8.42e-01 2.84e+01 ... (remaining 12178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.46: 5266 31.46 - 62.92: 110 62.92 - 94.38: 15 94.38 - 125.84: 0 125.84 - 157.30: 6 Dihedral angle restraints: 5397 sinusoidal: 2181 harmonic: 3216 Sorted by residual: dihedral pdb=" O2A ADP B 376 " pdb=" O3A ADP B 376 " pdb=" PA ADP B 376 " pdb=" PB ADP B 376 " ideal model delta sinusoidal sigma weight residual -60.00 97.30 -157.30 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O2A ADP C 376 " pdb=" O3A ADP C 376 " pdb=" PA ADP C 376 " pdb=" PB ADP C 376 " ideal model delta sinusoidal sigma weight residual -60.00 95.98 -155.98 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O2A ADP A 376 " pdb=" O3A ADP A 376 " pdb=" PA ADP A 376 " pdb=" PB ADP A 376 " ideal model delta sinusoidal sigma weight residual -60.00 95.66 -155.66 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 5394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1178 0.063 - 0.126: 159 0.126 - 0.188: 10 0.188 - 0.251: 4 0.251 - 0.314: 2 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA GLN B 137 " pdb=" N GLN B 137 " pdb=" C GLN B 137 " pdb=" CB GLN B 137 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA GLN A 137 " pdb=" N GLN A 137 " pdb=" C GLN A 137 " pdb=" CB GLN A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLN C 137 " pdb=" N GLN C 137 " pdb=" C GLN C 137 " pdb=" CB GLN C 137 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1350 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 202 " 0.012 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C THR A 202 " -0.045 2.00e-02 2.50e+03 pdb=" O THR A 202 " 0.018 2.00e-02 2.50e+03 pdb=" N THR A 203 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 202 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C THR C 202 " 0.043 2.00e-02 2.50e+03 pdb=" O THR C 202 " -0.017 2.00e-02 2.50e+03 pdb=" N THR C 203 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 180 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C LEU A 180 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU A 180 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 181 " 0.012 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 193 2.63 - 3.20: 8150 3.20 - 3.77: 15462 3.77 - 4.33: 22283 4.33 - 4.90: 34639 Nonbonded interactions: 80727 Sorted by model distance: nonbonded pdb="MG MG A 377 " pdb=" O HOH A 411 " model vdw 2.067 2.170 nonbonded pdb="MG MG C 377 " pdb=" O HOH C 411 " model vdw 2.068 2.170 nonbonded pdb="MG MG A 377 " pdb=" O HOH A 393 " model vdw 2.068 2.170 nonbonded pdb="MG MG B 377 " pdb=" O HOH B 388 " model vdw 2.069 2.170 nonbonded pdb="MG MG C 377 " pdb=" O HOH C 393 " model vdw 2.069 2.170 ... (remaining 80722 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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: 9.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.190 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.003 0.056 8976 Z= 0.215 Angle : 0.605 9.883 12183 Z= 0.324 Chirality : 0.046 0.314 1353 Planarity : 0.004 0.029 1557 Dihedral : 13.768 157.297 3339 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.64 % Allowed : 4.90 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.47 (0.27), residues: 1098 helix: 0.54 (0.25), residues: 459 sheet: 1.01 (0.36), residues: 207 loop : 1.82 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 79 HIS 0.001 0.000 HIS B 161 PHE 0.008 0.001 PHE C 255 TYR 0.008 0.001 TYR A 143 ARG 0.002 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 1.025 Fit side-chains REVERT: B 123 MET cc_start: 0.8103 (mmt) cc_final: 0.7789 (mmt) outliers start: 6 outliers final: 0 residues processed: 54 average time/residue: 1.8222 time to fit residues: 104.2518 Evaluate side-chains 48 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0060 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.0060 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.4414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN C 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.051420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.041591 restraints weight = 24550.723| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 2.42 r_work: 0.2513 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2385 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8976 Z= 0.139 Angle : 0.554 8.021 12183 Z= 0.266 Chirality : 0.043 0.191 1353 Planarity : 0.003 0.032 1557 Dihedral : 11.830 162.502 1251 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.75 % Allowed : 6.82 % Favored : 92.44 % 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: 1.73 (0.27), residues: 1098 helix: 0.87 (0.25), residues: 459 sheet: 1.03 (0.37), residues: 207 loop : 1.88 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 79 HIS 0.002 0.001 HIS B 161 PHE 0.006 0.001 PHE B 31 TYR 0.009 0.001 TYR B 143 ARG 0.005 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 1.161 Fit side-chains REVERT: B 44 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.6369 (pmt) REVERT: C 72 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8015 (tm-30) outliers start: 7 outliers final: 1 residues processed: 52 average time/residue: 1.7029 time to fit residues: 94.4807 Evaluate side-chains 51 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 72 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 69 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.048790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.038848 restraints weight = 24810.354| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 2.44 r_work: 0.2437 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2309 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8976 Z= 0.254 Angle : 0.574 7.475 12183 Z= 0.279 Chirality : 0.046 0.173 1353 Planarity : 0.004 0.039 1557 Dihedral : 11.698 166.346 1251 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.17 % Allowed : 5.96 % Favored : 92.86 % 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: 1.85 (0.27), residues: 1098 helix: 0.94 (0.26), residues: 462 sheet: 1.31 (0.39), residues: 201 loop : 1.82 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE A 262 TYR 0.014 0.001 TYR B 143 ARG 0.003 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 1.024 Fit side-chains REVERT: B 44 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.6301 (pmt) REVERT: C 227 MET cc_start: 0.8807 (mmm) cc_final: 0.8520 (mmt) outliers start: 11 outliers final: 4 residues processed: 55 average time/residue: 1.5262 time to fit residues: 89.9356 Evaluate side-chains 53 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain C residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS B 40 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.049789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.039917 restraints weight = 24576.304| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 2.43 r_work: 0.2472 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2345 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8976 Z= 0.152 Angle : 0.527 6.830 12183 Z= 0.250 Chirality : 0.043 0.152 1353 Planarity : 0.003 0.038 1557 Dihedral : 11.645 167.757 1251 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.85 % Allowed : 7.56 % Favored : 91.59 % 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: 1.93 (0.27), residues: 1098 helix: 1.03 (0.25), residues: 465 sheet: 1.28 (0.39), residues: 201 loop : 1.89 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.002 0.001 HIS A 161 PHE 0.007 0.001 PHE C 255 TYR 0.010 0.001 TYR B 143 ARG 0.002 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.079 Fit side-chains REVERT: B 44 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.6267 (pmt) outliers start: 8 outliers final: 1 residues processed: 52 average time/residue: 1.6578 time to fit residues: 91.9518 Evaluate side-chains 51 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain B residue 44 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.047267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.037538 restraints weight = 24978.005| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 2.42 r_work: 0.2400 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2271 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 8976 Z= 0.413 Angle : 0.612 7.542 12183 Z= 0.301 Chirality : 0.049 0.177 1353 Planarity : 0.004 0.042 1557 Dihedral : 11.769 166.076 1251 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.17 % Allowed : 7.03 % Favored : 91.80 % 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: 1.72 (0.27), residues: 1098 helix: 0.95 (0.26), residues: 462 sheet: 1.34 (0.39), residues: 198 loop : 1.55 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 79 HIS 0.005 0.001 HIS A 161 PHE 0.011 0.001 PHE A 262 TYR 0.010 0.001 TYR B 143 ARG 0.003 0.001 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 1.122 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 55 average time/residue: 1.5873 time to fit residues: 93.2392 Evaluate side-chains 52 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain C residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.049159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.039405 restraints weight = 24628.432| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 2.42 r_work: 0.2462 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2333 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8976 Z= 0.153 Angle : 0.528 6.835 12183 Z= 0.251 Chirality : 0.044 0.152 1353 Planarity : 0.003 0.037 1557 Dihedral : 11.676 170.178 1251 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.64 % Allowed : 7.56 % Favored : 91.80 % 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: 1.87 (0.27), residues: 1098 helix: 1.10 (0.26), residues: 465 sheet: 1.32 (0.39), residues: 198 loop : 1.66 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.003 0.001 HIS B 161 PHE 0.008 0.001 PHE C 255 TYR 0.007 0.001 TYR B 143 ARG 0.002 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.935 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 1.8448 time to fit residues: 101.7142 Evaluate side-chains 51 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.048628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.038774 restraints weight = 24941.623| |-----------------------------------------------------------------------------| r_work (start): 0.2567 rms_B_bonded: 2.45 r_work: 0.2440 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2312 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8976 Z= 0.223 Angle : 0.546 6.864 12183 Z= 0.261 Chirality : 0.045 0.153 1353 Planarity : 0.003 0.038 1557 Dihedral : 11.642 169.154 1251 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.85 % Allowed : 7.67 % Favored : 91.48 % 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: 1.89 (0.27), residues: 1098 helix: 1.18 (0.26), residues: 462 sheet: 1.32 (0.39), residues: 198 loop : 1.59 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 340 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE C 255 TYR 0.009 0.001 TYR B 143 ARG 0.002 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.054 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 1.5937 time to fit residues: 90.2772 Evaluate side-chains 54 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain C residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.048906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.039030 restraints weight = 25204.894| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 2.47 r_work: 0.2450 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2321 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8976 Z= 0.193 Angle : 0.536 6.728 12183 Z= 0.255 Chirality : 0.044 0.148 1353 Planarity : 0.003 0.037 1557 Dihedral : 11.616 170.072 1251 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.85 % Allowed : 7.99 % Favored : 91.16 % 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: 1.92 (0.27), residues: 1098 helix: 1.22 (0.26), residues: 462 sheet: 1.31 (0.38), residues: 198 loop : 1.61 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.003 0.001 HIS B 161 PHE 0.008 0.001 PHE C 255 TYR 0.008 0.001 TYR B 143 ARG 0.002 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.024 Fit side-chains REVERT: B 44 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.6467 (pmt) outliers start: 8 outliers final: 5 residues processed: 53 average time/residue: 1.5474 time to fit residues: 87.6578 Evaluate side-chains 54 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain C residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.048513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.038674 restraints weight = 24818.604| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 2.44 r_work: 0.2438 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2310 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8976 Z= 0.235 Angle : 0.548 6.774 12183 Z= 0.262 Chirality : 0.045 0.152 1353 Planarity : 0.003 0.037 1557 Dihedral : 11.613 169.803 1251 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.85 % Allowed : 7.88 % Favored : 91.27 % 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: 1.89 (0.27), residues: 1098 helix: 1.20 (0.25), residues: 462 sheet: 1.32 (0.38), residues: 198 loop : 1.57 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE C 255 TYR 0.009 0.001 TYR B 143 ARG 0.002 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.025 Fit side-chains REVERT: B 44 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.6651 (pmt) REVERT: C 314 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8699 (tp40) outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 1.5743 time to fit residues: 90.6926 Evaluate side-chains 55 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.047545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.037779 restraints weight = 25208.874| |-----------------------------------------------------------------------------| r_work (start): 0.2540 rms_B_bonded: 2.44 r_work: 0.2411 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2283 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 8976 Z= 0.337 Angle : 0.584 7.088 12183 Z= 0.284 Chirality : 0.047 0.162 1353 Planarity : 0.004 0.037 1557 Dihedral : 11.688 169.829 1251 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.85 % Allowed : 7.88 % Favored : 91.27 % 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: 1.75 (0.27), residues: 1098 helix: 1.08 (0.25), residues: 462 sheet: 1.31 (0.38), residues: 198 loop : 1.47 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 340 HIS 0.004 0.001 HIS A 161 PHE 0.010 0.001 PHE C 255 TYR 0.010 0.001 TYR B 143 ARG 0.003 0.000 ARG B 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.869 Fit side-chains REVERT: C 314 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8619 (tp40) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 1.5954 time to fit residues: 91.8656 Evaluate side-chains 55 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.047884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.038145 restraints weight = 24981.090| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 2.43 r_work: 0.2423 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2294 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8976 Z= 0.283 Angle : 0.565 7.154 12183 Z= 0.273 Chirality : 0.046 0.161 1353 Planarity : 0.004 0.037 1557 Dihedral : 11.691 170.585 1251 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.75 % Allowed : 7.99 % Favored : 91.27 % 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: 1.80 (0.27), residues: 1098 helix: 1.16 (0.25), residues: 459 sheet: 1.25 (0.37), residues: 204 loop : 1.49 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 340 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE C 255 TYR 0.009 0.001 TYR B 143 ARG 0.002 0.000 ARG B 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6462.79 seconds wall clock time: 115 minutes 1.07 seconds (6901.07 seconds total)