Starting phenix.real_space_refine on Sun Dec 29 00:27:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d13_27114/12_2024/8d13_27114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d13_27114/12_2024/8d13_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_27114/12_2024/8d13_27114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d13_27114/12_2024/8d13_27114.map" model { file = "/net/cci-nas-00/data/ceres_data/8d13_27114/12_2024/8d13_27114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d13_27114/12_2024/8d13_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-5532/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: 10.22, per 1000 atoms: 1.11 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: 2.32 Conformation dependent library (CDL) restraints added in 1.0 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: 1.25 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: 2.99 Time building geometry restraints manager: 2.67 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.470 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.550 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.830 ------------------------------------------------------------------------------- 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 : 1.222 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: 1.8705 time to fit residues: 106.8968 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 : 1.130 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 1.238 Fit side-chains REVERT: B 44 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.6702 (pmt) outliers start: 7 outliers final: 1 residues processed: 52 average time/residue: 1.7950 time to fit residues: 99.4651 Evaluate side-chains 50 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 41 GLN C 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1443 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= 0.396 Angle : 0.626 8.007 12183 Z= 0.310 Chirality : 0.049 0.198 1353 Planarity : 0.004 0.042 1557 Dihedral : 11.832 165.971 1251 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.17 % Allowed : 5.86 % Favored : 92.97 % 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: 1.69 (0.27), residues: 1098 helix: 0.87 (0.26), residues: 459 sheet: 1.14 (0.38), residues: 207 loop : 1.72 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 79 HIS 0.004 0.001 HIS A 161 PHE 0.011 0.001 PHE A 262 TYR 0.013 0.001 TYR B 143 ARG 0.003 0.001 ARG B 254 *********************** 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 : 0.950 Fit side-chains REVERT: C 227 MET cc_start: 0.8349 (mmm) cc_final: 0.8012 (mmm) outliers start: 11 outliers final: 5 residues processed: 55 average time/residue: 1.5098 time to fit residues: 88.9898 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 : 1.082 ------------------------------------------------------------------------------- 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 75 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1503 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= 0.204 Angle : 0.547 7.285 12183 Z= 0.263 Chirality : 0.045 0.166 1353 Planarity : 0.003 0.038 1557 Dihedral : 11.758 168.787 1251 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.06 % Allowed : 7.03 % 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: 1.79 (0.27), residues: 1098 helix: 0.97 (0.26), residues: 462 sheet: 1.38 (0.39), residues: 198 loop : 1.63 (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 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 58 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 1.163 Fit side-chains REVERT: C 227 MET cc_start: 0.8287 (mmm) cc_final: 0.8069 (mmm) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 1.5307 time to fit residues: 91.9118 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 : 1.093 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1626 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= 0.270 Angle : 0.564 7.243 12183 Z= 0.272 Chirality : 0.046 0.166 1353 Planarity : 0.004 0.039 1557 Dihedral : 11.732 168.966 1251 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.28 % Allowed : 6.82 % 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: 1.78 (0.27), residues: 1098 helix: 1.02 (0.26), residues: 462 sheet: 1.37 (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 0.004 0.001 HIS A 161 PHE 0.009 0.001 PHE C 255 TYR 0.010 0.001 TYR B 143 ARG 0.003 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: 12 poor density : 49 time to evaluate : 1.209 Fit side-chains REVERT: C 227 MET cc_start: 0.8313 (mmm) cc_final: 0.7936 (mmm) REVERT: C 355 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7292 (mtm) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 1.6438 time to fit residues: 100.0311 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 : 1.097 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8976 Z= 0.201 Angle : 0.543 6.948 12183 Z= 0.260 Chirality : 0.044 0.156 1353 Planarity : 0.003 0.036 1557 Dihedral : 11.700 170.384 1251 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.06 % Allowed : 7.03 % 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: 1.83 (0.27), residues: 1098 helix: 1.11 (0.26), residues: 462 sheet: 1.36 (0.39), residues: 198 loop : 1.55 (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 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 59 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 2.057 Fit side-chains REVERT: C 227 MET cc_start: 0.8291 (mmm) cc_final: 0.7897 (mmm) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 1.6733 time to fit residues: 96.7179 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 : 1.106 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.0670 chunk 90 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.0010 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5728 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8976 Z= 0.143 Angle : 0.521 6.615 12183 Z= 0.246 Chirality : 0.043 0.145 1353 Planarity : 0.003 0.036 1557 Dihedral : 11.629 171.266 1251 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.53 % Allowed : 7.67 % 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: 1.97 (0.27), residues: 1098 helix: 1.26 (0.26), residues: 462 sheet: 1.37 (0.39), residues: 198 loop : 1.62 (0.34), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 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 0.001 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 53 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 1.080 Fit side-chains REVERT: C 227 MET cc_start: 0.8260 (mmm) cc_final: 0.8021 (mmm) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 1.6342 time to fit residues: 87.2901 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 : 1.104 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1776 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= 0.294 Angle : 0.566 6.989 12183 Z= 0.273 Chirality : 0.046 0.159 1353 Planarity : 0.004 0.037 1557 Dihedral : 11.666 169.804 1251 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: 1.84 (0.27), residues: 1098 helix: 1.16 (0.25), 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 0.012 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 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 : 0.877 Fit side-chains REVERT: C 227 MET cc_start: 0.8318 (mmm) cc_final: 0.7929 (mmm) outliers start: 8 outliers final: 5 residues processed: 53 average time/residue: 1.5947 time to fit residues: 90.3050 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 : 1.017 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 78 optimal weight: 0.0020 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8976 Z= 0.120 Angle : 0.516 6.495 12183 Z= 0.242 Chirality : 0.043 0.141 1353 Planarity : 0.003 0.035 1557 Dihedral : 11.586 172.265 1251 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.53 % Allowed : 8.09 % Favored : 91.37 % 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: 2.01 (0.27), residues: 1098 helix: 1.28 (0.26), residues: 465 sheet: 1.35 (0.39), residues: 198 loop : 1.69 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.002 0.000 HIS B 161 PHE 0.008 0.001 PHE C 255 TYR 0.007 0.001 TYR A 69 ARG 0.001 0.000 ARG C 335 *********************** 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 53 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 1.120 Fit side-chains REVERT: B 44 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.6884 (pmt) REVERT: C 227 MET cc_start: 0.8236 (mmm) cc_final: 0.7994 (mmm) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 1.7194 time to fit residues: 93.6264 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 : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.0370 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.0050 overall best weight: 0.4250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8976 Z= 0.128 Angle : 0.515 6.380 12183 Z= 0.240 Chirality : 0.043 0.141 1353 Planarity : 0.003 0.036 1557 Dihedral : 11.445 172.062 1251 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.32 % Allowed : 8.41 % 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: 2.10 (0.27), residues: 1098 helix: 1.39 (0.26), residues: 465 sheet: 1.34 (0.39), residues: 198 loop : 1.71 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.002 0.001 HIS B 161 PHE 0.007 0.001 PHE C 255 TYR 0.007 0.001 TYR B 143 ARG 0.001 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 51 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 1.097 Fit side-chains REVERT: B 44 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.6878 (pmt) REVERT: C 227 MET cc_start: 0.8202 (mmm) cc_final: 0.7943 (mmm) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 1.6406 time to fit residues: 86.1914 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 : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.2872 r_free = 0.2872 target = 0.049063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.039266 restraints weight = 24597.349| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 2.43 r_work: 0.2461 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2332 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1847 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= 0.189 Angle : 0.532 6.503 12183 Z= 0.251 Chirality : 0.044 0.149 1353 Planarity : 0.003 0.036 1557 Dihedral : 11.396 171.898 1251 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.53 % Allowed : 8.31 % 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: 2.06 (0.27), residues: 1098 helix: 1.36 (0.26), residues: 465 sheet: 1.33 (0.39), residues: 198 loop : 1.67 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3024.11 seconds wall clock time: 55 minutes 31.35 seconds (3331.35 seconds total)