Starting phenix.real_space_refine on Fri Mar 14 01:29:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d13_27114/03_2025/8d13_27114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d13_27114/03_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_27114/03_2025/8d13_27114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d13_27114/03_2025/8d13_27114.map" model { file = "/net/cci-nas-00/data/ceres_data/8d13_27114/03_2025/8d13_27114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d13_27114/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 8.21, per 1000 atoms: 0.89 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.33 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: 3.27 Time building geometry restraints manager: 2.69 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: 0.05 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: 13.320 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.520 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.370 ------------------------------------------------------------------------------- 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 : 0.981 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: 1.6992 time to fit residues: 97.3579 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 : 1.122 ------------------------------------------------------------------------------- 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 = 0.051422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.041597 restraints weight = 24551.303| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 2.41 r_work: 0.2513 rms_B_bonded: 2.76 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: 0.0946 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 8.027 12183 Z= 0.266 Chirality : 0.043 0.192 1353 Planarity : 0.003 0.032 1557 Dihedral : 11.831 162.483 1251 Min Nonbonded Distance : 1.948 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 : 1.523 Fit side-chains REVERT: B 44 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.6369 (pmt) REVERT: C 72 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8016 (tm-30) outliers start: 7 outliers final: 1 residues processed: 52 average time/residue: 2.0621 time to fit residues: 114.5321 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 : 1.180 ------------------------------------------------------------------------------- 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: 0.8980 chunk 6 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.2839 r_free = 0.2839 target = 0.048127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.038251 restraints weight = 24877.385| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 2.43 r_work: 0.2420 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2291 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1379 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= 0.317 Angle : 0.599 7.715 12183 Z= 0.294 Chirality : 0.047 0.192 1353 Planarity : 0.004 0.041 1557 Dihedral : 11.759 165.927 1251 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.28 % Allowed : 5.86 % 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: 1.76 (0.27), residues: 1098 helix: 0.89 (0.26), residues: 462 sheet: 1.28 (0.39), residues: 201 loop : 1.75 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.004 0.001 HIS C 161 PHE 0.011 0.001 PHE A 262 TYR 0.014 0.001 TYR B 143 ARG 0.004 0.001 ARG A 177 *********************** 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 60 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 1.004 Fit side-chains REVERT: B 44 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.6301 (pmt) REVERT: C 227 MET cc_start: 0.8849 (mmm) cc_final: 0.8573 (mmm) outliers start: 12 outliers final: 4 residues processed: 56 average time/residue: 1.5043 time to fit residues: 90.2191 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 : 1.209 ------------------------------------------------------------------------------- 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: 0.0870 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.2878 r_free = 0.2878 target = 0.049620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.039720 restraints weight = 24593.042| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 2.43 r_work: 0.2466 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2338 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 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= 0.161 Angle : 0.531 6.946 12183 Z= 0.253 Chirality : 0.044 0.158 1353 Planarity : 0.003 0.038 1557 Dihedral : 11.696 168.349 1251 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.96 % Allowed : 7.35 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.26), residues: 462 sheet: 1.28 (0.39), residues: 201 loop : 1.79 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 79 HIS 0.002 0.001 HIS C 161 PHE 0.008 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 57 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 1.024 Fit side-chains REVERT: B 44 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.6257 (pmt) outliers start: 9 outliers final: 1 residues processed: 53 average time/residue: 1.4642 time to fit residues: 83.0434 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 : 1.055 ------------------------------------------------------------------------------- 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: 0.8980 chunk 65 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.2840 r_free = 0.2840 target = 0.048045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.038156 restraints weight = 24778.192| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 2.43 r_work: 0.2419 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2290 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1591 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= 0.326 Angle : 0.578 7.260 12183 Z= 0.281 Chirality : 0.047 0.169 1353 Planarity : 0.004 0.040 1557 Dihedral : 11.726 167.075 1251 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.38 % Allowed : 6.92 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.81 (0.27), residues: 1098 helix: 1.02 (0.26), residues: 462 sheet: 1.38 (0.39), residues: 198 loop : 1.60 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.002 0.000 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 61 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.997 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 56 average time/residue: 1.4344 time to fit residues: 86.1143 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 : 1.059 ------------------------------------------------------------------------------- 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: 3.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.2834 r_free = 0.2834 target = 0.047716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.038012 restraints weight = 24799.323| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 2.41 r_work: 0.2417 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2287 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1690 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= 0.313 Angle : 0.574 7.383 12183 Z= 0.279 Chirality : 0.047 0.168 1353 Planarity : 0.004 0.038 1557 Dihedral : 11.783 169.389 1251 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.85 % Allowed : 7.24 % Favored : 91.91 % 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: 1.68 (0.27), residues: 1098 helix: 0.98 (0.25), residues: 462 sheet: 1.32 (0.39), residues: 198 loop : 1.46 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 79 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 0.003 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 57 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 1.146 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 1.8397 time to fit residues: 106.2143 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 : 0.955 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.2853 r_free = 0.2853 target = 0.048436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.038568 restraints weight = 24877.808| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 2.44 r_work: 0.2433 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2304 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8976 Z= 0.219 Angle : 0.552 7.085 12183 Z= 0.265 Chirality : 0.045 0.158 1353 Planarity : 0.003 0.037 1557 Dihedral : 11.733 170.166 1251 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: 1.78 (0.27), residues: 1098 helix: 1.10 (0.26), residues: 462 sheet: 1.33 (0.39), residues: 198 loop : 1.47 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 79 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE C 255 TYR 0.008 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 57 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 1.040 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 2.0478 time to fit residues: 119.0779 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 : 1.237 ------------------------------------------------------------------------------- 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: 2.9990 chunk 25 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.048905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.039035 restraints weight = 25159.450| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 2.46 r_work: 0.2450 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2320 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8976 Z= 0.173 Angle : 0.532 6.753 12183 Z= 0.252 Chirality : 0.044 0.148 1353 Planarity : 0.003 0.037 1557 Dihedral : 11.661 171.090 1251 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.96 % Allowed : 7.77 % 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: 1.87 (0.27), residues: 1098 helix: 1.20 (0.26), residues: 462 sheet: 1.34 (0.39), residues: 198 loop : 1.52 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 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 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 57 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 1.408 Fit side-chains REVERT: B 44 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.6629 (pmt) REVERT: C 314 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8710 (tp40) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 1.5548 time to fit residues: 89.8193 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 : 0.976 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.2846 r_free = 0.2846 target = 0.048101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.038266 restraints weight = 24890.636| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 2.44 r_work: 0.2426 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2297 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1794 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= 0.264 Angle : 0.557 6.922 12183 Z= 0.268 Chirality : 0.045 0.157 1353 Planarity : 0.004 0.037 1557 Dihedral : 11.672 170.168 1251 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.75 % Allowed : 8.09 % 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: 1.82 (0.27), residues: 1098 helix: 1.16 (0.26), residues: 462 sheet: 1.33 (0.39), residues: 198 loop : 1.48 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 *********************** 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 55 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 1.042 Fit side-chains REVERT: C 314 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8719 (tp40) outliers start: 7 outliers final: 6 residues processed: 53 average time/residue: 1.4732 time to fit residues: 83.6327 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 : 0.930 ------------------------------------------------------------------------------- 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: 4.9990 chunk 67 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.2846 r_free = 0.2846 target = 0.048065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.038242 restraints weight = 24966.840| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 2.44 r_work: 0.2425 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2296 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1817 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= 0.269 Angle : 0.560 7.023 12183 Z= 0.270 Chirality : 0.046 0.158 1353 Planarity : 0.004 0.037 1557 Dihedral : 11.694 170.859 1251 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: 1.79 (0.27), residues: 1098 helix: 1.13 (0.25), residues: 462 sheet: 1.33 (0.39), residues: 198 loop : 1.46 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE C 255 TYR 0.008 0.001 TYR B 143 ARG 0.002 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 : 0.963 Fit side-chains REVERT: C 314 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8732 (tp40) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 1.4632 time to fit residues: 84.4725 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 : 0.955 ------------------------------------------------------------------------------- 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: 3.9990 chunk 99 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 = 0.2843 r_free = 0.2843 target = 0.048033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.038159 restraints weight = 24910.754| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 2.48 r_work: 0.2422 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2289 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1832 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= 0.257 Angle : 0.556 7.017 12183 Z= 0.267 Chirality : 0.045 0.158 1353 Planarity : 0.004 0.037 1557 Dihedral : 11.689 170.999 1251 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 1.81 (0.27), residues: 1098 helix: 1.16 (0.26), residues: 462 sheet: 1.34 (0.39), residues: 198 loop : 1.46 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 340 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE C 255 TYR 0.008 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: 6763.37 seconds wall clock time: 120 minutes 8.63 seconds (7208.63 seconds total)