Starting phenix.real_space_refine on Thu Jul 2 17:22:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d14_27115/07_2026/8d14_27115.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d14_27115/07_2026/8d14_27115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8d14_27115/07_2026/8d14_27115.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d14_27115/07_2026/8d14_27115.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d14_27115/07_2026/8d14_27115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d14_27115/07_2026/8d14_27115.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d14_27115/07_2026/8d14_27115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d14_27115/07_2026/8d14_27115.map" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 9 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 5541 2.51 5 N 1482 2.21 5 O 2127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9225 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "C" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Time building chain proxies: 2.10, per 1000 atoms: 0.23 Number of scatterers: 9225 At special positions: 0 Unit cell: (89.61, 85.49, 139.05, 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 9 15.00 Mg 3 11.99 O 2127 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: 0.77 Conformation dependent library (CDL) restraints added in 330.5 milliseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 18 sheets defined 51.8% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 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 removed outlier: 3.617A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.029A 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: 3.668A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 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 348 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.981A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.846A 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 removed outlier: 3.617A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.029A 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 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: 3.668A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 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 348 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.981A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.846A 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 removed outlier: 3.617A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.029A 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 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: 3.668A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 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 348 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.983A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.845A 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: 6.691A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.296A 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: 6.492A 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: 6.692A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.296A 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 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.491A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (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: 6.690A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.294A 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: 6.492A 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 241 453 hydrogen bonds defined for protein. 1143 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: 1.74 Time building geometry restraints manager: 1.01 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: 1599 1.32 - 1.45: 2228 1.45 - 1.57: 5041 1.57 - 1.69: 9 1.69 - 1.81: 111 Bond restraints: 8988 Sorted by residual: bond pdb=" O3 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" O4 PO4 B 403 " pdb=" P PO4 B 403 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 9.05e+00 bond pdb=" O3 PO4 B 403 " pdb=" P PO4 B 403 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" O3 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.88e+00 bond pdb=" O2 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.68e+00 ... (remaining 8983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 11995 1.74 - 3.49: 159 3.49 - 5.23: 25 5.23 - 6.97: 17 6.97 - 8.72: 5 Bond angle restraints: 12201 Sorted by residual: angle pdb=" N GLN B 137 " pdb=" CA GLN B 137 " pdb=" C GLN B 137 " ideal model delta sigma weight residual 111.33 118.60 -7.27 1.21e+00 6.83e-01 3.61e+01 angle pdb=" N GLN A 137 " pdb=" CA GLN A 137 " pdb=" C GLN A 137 " ideal model delta sigma weight residual 111.33 117.10 -5.77 1.21e+00 6.83e-01 2.27e+01 angle pdb=" N GLN C 137 " pdb=" CA GLN C 137 " pdb=" C GLN C 137 " ideal model delta sigma weight residual 111.33 116.50 -5.17 1.21e+00 6.83e-01 1.82e+01 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 113.71 110.56 3.15 9.50e-01 1.11e+00 1.10e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 113.71 110.56 3.15 9.50e-01 1.11e+00 1.10e+01 ... (remaining 12196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.90: 5268 30.90 - 61.79: 108 61.79 - 92.69: 12 92.69 - 123.59: 3 123.59 - 154.49: 6 Dihedral angle restraints: 5397 sinusoidal: 2181 harmonic: 3216 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 94.49 -154.49 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 90.10 -150.10 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.60 -149.60 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 5394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1210 0.073 - 0.147: 136 0.147 - 0.220: 4 0.220 - 0.294: 0 0.294 - 0.367: 3 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 2.14 0.37 2.00e-01 2.50e+01 3.37e+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 2.19 0.32 2.00e-01 2.50e+01 2.51e+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 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 1350 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 134 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C VAL C 134 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL C 134 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA C 135 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 134 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C VAL A 134 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL A 134 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA A 135 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 321 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO C 322 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " 0.018 5.00e-02 4.00e+02 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 241 2.63 - 3.20: 8166 3.20 - 3.77: 15876 3.77 - 4.33: 22864 4.33 - 4.90: 34840 Nonbonded interactions: 81987 Sorted by model distance: nonbonded pdb="MG MG C 402 " pdb=" O HOH C 546 " model vdw 2.064 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 548 " model vdw 2.066 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 587 " model vdw 2.067 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 562 " model vdw 2.067 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 594 " model vdw 2.068 2.170 ... (remaining 81982 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: 0.03 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: 10.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.840 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 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 : 0.004 0.061 8988 Z= 0.226 Angle : 0.572 8.716 12201 Z= 0.296 Chirality : 0.046 0.367 1353 Planarity : 0.003 0.033 1557 Dihedral : 13.460 154.485 3339 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.32 % Allowed : 3.83 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.26), residues: 1098 helix: 0.82 (0.26), residues: 459 sheet: 0.38 (0.34), residues: 207 loop : 1.79 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 210 TYR 0.010 0.001 TYR C 143 PHE 0.008 0.001 PHE A 255 TRP 0.005 0.001 TRP C 340 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.23 ( 8988) covalent geometry : angle 0.57236 / 0.30 (12201) hydrogen bonds : bond 0.17219 / 11.99 ( 447) hydrogen bonds : angle 6.47779 / 4.57 ( 1143) *********************** 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 109 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.281 Fit side-chains REVERT: A 82 MET cc_start: 0.9046 (tpt) cc_final: 0.8730 (tpt) REVERT: B 305 MET cc_start: 0.8353 (mmm) cc_final: 0.8017 (mmm) REVERT: C 44 MET cc_start: 0.8146 (mtp) cc_final: 0.7730 (mtp) REVERT: C 82 MET cc_start: 0.8974 (tpt) cc_final: 0.8650 (tpt) REVERT: C 227 MET cc_start: 0.8453 (mmm) cc_final: 0.8164 (mmm) REVERT: C 364 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6276 (mm-30) outliers start: 3 outliers final: 0 residues processed: 109 average time/residue: 0.8261 time to fit residues: 94.3089 Evaluate side-chains 68 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN B 353 GLN C 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.085393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.069995 restraints weight = 13290.110| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.57 r_work: 0.2769 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8988 Z= 0.242 Angle : 0.673 8.529 12201 Z= 0.336 Chirality : 0.052 0.208 1353 Planarity : 0.005 0.037 1557 Dihedral : 11.872 165.245 1251 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.38 % Allowed : 7.14 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1098 helix: 0.58 (0.25), residues: 465 sheet: 0.61 (0.36), residues: 201 loop : 1.68 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 28 TYR 0.010 0.002 TYR B 143 PHE 0.015 0.002 PHE A 262 TRP 0.013 0.003 TRP B 79 HIS 0.007 0.002 HIS C 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 ( 8988) covalent geometry : angle 0.67256 / 0.34 (12201) hydrogen bonds : bond 0.05131 / 3.47 ( 447) hydrogen bonds : angle 4.98385 / 3.56 ( 1143) *********************** 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 80 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7872 (p0) cc_final: 0.7548 (p0) REVERT: A 64 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8710 (pp) REVERT: A 82 MET cc_start: 0.9280 (tpt) cc_final: 0.9054 (tpt) REVERT: B 123 MET cc_start: 0.9169 (mmp) cc_final: 0.8861 (tpt) REVERT: B 305 MET cc_start: 0.9019 (mmm) cc_final: 0.8793 (mmm) REVERT: B 355 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: C 47 MET cc_start: 0.6213 (pmm) cc_final: 0.5826 (pmm) REVERT: C 82 MET cc_start: 0.9264 (tpt) cc_final: 0.8986 (tpt) REVERT: C 227 MET cc_start: 0.8651 (mmm) cc_final: 0.8347 (mmm) REVERT: C 354 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.8019 (tp40) REVERT: C 355 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8230 (mtp) REVERT: C 360 GLN cc_start: 0.7798 (tm-30) cc_final: 0.6679 (tm-30) REVERT: C 364 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7111 (mt-10) outliers start: 13 outliers final: 5 residues processed: 76 average time/residue: 0.7519 time to fit residues: 60.1141 Evaluate side-chains 73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 ASN B 263 GLN C 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.087145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.071765 restraints weight = 13248.670| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.58 r_work: 0.2808 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8988 Z= 0.118 Angle : 0.561 7.710 12201 Z= 0.271 Chirality : 0.045 0.180 1353 Planarity : 0.004 0.033 1557 Dihedral : 11.593 165.610 1251 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.38 % Allowed : 7.88 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.26), residues: 1098 helix: 0.82 (0.25), residues: 465 sheet: 0.71 (0.36), residues: 201 loop : 1.69 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 28 TYR 0.008 0.001 TYR C 143 PHE 0.008 0.001 PHE B 31 TRP 0.011 0.002 TRP B 79 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8988) covalent geometry : angle 0.56115 / 0.27 (12201) hydrogen bonds : bond 0.03508 / 2.34 ( 447) hydrogen bonds : angle 4.61784 / 3.29 ( 1143) *********************** 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 81 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7803 (p0) cc_final: 0.7567 (p0) REVERT: A 314 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: B 305 MET cc_start: 0.9016 (mmm) cc_final: 0.8781 (mmm) REVERT: B 355 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8287 (mtm) REVERT: C 47 MET cc_start: 0.6347 (pmm) cc_final: 0.5965 (pmm) REVERT: C 82 MET cc_start: 0.9222 (tpt) cc_final: 0.8914 (tpt) REVERT: C 227 MET cc_start: 0.8645 (mmm) cc_final: 0.8300 (mmm) REVERT: C 241 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: C 354 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8038 (tp40) REVERT: C 355 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8198 (mtp) REVERT: C 360 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7487 (tm-30) outliers start: 13 outliers final: 5 residues processed: 76 average time/residue: 0.7118 time to fit residues: 56.8083 Evaluate side-chains 74 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 372 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.087030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.071755 restraints weight = 13433.802| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.59 r_work: 0.2810 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8988 Z= 0.118 Angle : 0.555 7.386 12201 Z= 0.266 Chirality : 0.045 0.169 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.525 166.616 1251 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.49 % Allowed : 8.31 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.26), residues: 1098 helix: 0.93 (0.25), residues: 465 sheet: 0.77 (0.37), residues: 201 loop : 1.71 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 28 TYR 0.008 0.001 TYR C 143 PHE 0.009 0.001 PHE C 255 TRP 0.011 0.002 TRP B 79 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8988) covalent geometry : angle 0.55529 / 0.27 (12201) hydrogen bonds : bond 0.03420 / 2.29 ( 447) hydrogen bonds : angle 4.50669 / 3.21 ( 1143) *********************** 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 78 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8676 (pp) REVERT: A 314 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8569 (tp40) REVERT: A 328 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8418 (ttmp) REVERT: B 305 MET cc_start: 0.9004 (mmm) cc_final: 0.8759 (mmm) REVERT: B 355 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8257 (mtm) REVERT: C 82 MET cc_start: 0.9220 (tpt) cc_final: 0.8878 (tpt) REVERT: C 227 MET cc_start: 0.8641 (mmm) cc_final: 0.8255 (mmm) REVERT: C 241 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: C 353 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8148 (mp-120) REVERT: C 354 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7988 (tp40) REVERT: C 355 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8070 (mtp) REVERT: C 360 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7438 (tm-30) outliers start: 14 outliers final: 5 residues processed: 72 average time/residue: 0.7218 time to fit residues: 54.6054 Evaluate side-chains 76 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 372 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.087200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.071887 restraints weight = 13438.208| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.58 r_work: 0.2812 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8988 Z= 0.114 Angle : 0.549 7.293 12201 Z= 0.262 Chirality : 0.045 0.167 1353 Planarity : 0.004 0.032 1557 Dihedral : 11.508 166.839 1251 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.60 % Allowed : 8.52 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.26), residues: 1098 helix: 0.97 (0.25), residues: 465 sheet: 0.80 (0.37), residues: 201 loop : 1.70 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.008 0.001 TYR C 143 PHE 0.008 0.001 PHE B 31 TRP 0.011 0.002 TRP B 79 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 8988) covalent geometry : angle 0.54944 / 0.26 (12201) hydrogen bonds : bond 0.03304 / 2.22 ( 447) hydrogen bonds : angle 4.45419 / 3.17 ( 1143) *********************** 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 80 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8684 (pp) REVERT: A 314 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8570 (tp40) REVERT: A 328 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8439 (ttmp) REVERT: B 305 MET cc_start: 0.9007 (mmm) cc_final: 0.8758 (mmm) REVERT: B 355 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8261 (mtm) REVERT: C 82 MET cc_start: 0.9220 (tpt) cc_final: 0.8872 (tpt) REVERT: C 227 MET cc_start: 0.8636 (mmm) cc_final: 0.8236 (mmm) REVERT: C 241 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: C 354 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8034 (tp40) REVERT: C 355 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8094 (mtp) REVERT: C 360 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7430 (tm-30) outliers start: 15 outliers final: 6 residues processed: 72 average time/residue: 0.7447 time to fit residues: 56.2730 Evaluate side-chains 76 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 372 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.087165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.071859 restraints weight = 13377.098| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.58 r_work: 0.2812 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8988 Z= 0.113 Angle : 0.548 7.234 12201 Z= 0.261 Chirality : 0.045 0.166 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.504 167.291 1251 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.81 % Allowed : 8.63 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.26), residues: 1098 helix: 1.00 (0.25), residues: 465 sheet: 0.79 (0.37), residues: 201 loop : 1.72 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.007 0.001 TYR C 143 PHE 0.008 0.001 PHE C 255 TRP 0.011 0.002 TRP B 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 8988) covalent geometry : angle 0.54776 / 0.26 (12201) hydrogen bonds : bond 0.03253 / 2.19 ( 447) hydrogen bonds : angle 4.42541 / 3.15 ( 1143) *********************** 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 81 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8684 (pp) REVERT: A 314 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8567 (tp40) REVERT: A 328 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8442 (ttmp) REVERT: B 305 MET cc_start: 0.9001 (mmm) cc_final: 0.8744 (mmm) REVERT: B 355 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8273 (mtm) REVERT: C 82 MET cc_start: 0.9222 (tpt) cc_final: 0.8981 (tpt) REVERT: C 227 MET cc_start: 0.8619 (mmm) cc_final: 0.8231 (mmm) REVERT: C 241 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: C 354 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7970 (tp40) REVERT: C 355 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8071 (mtp) REVERT: C 360 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7353 (tm-30) outliers start: 17 outliers final: 8 residues processed: 73 average time/residue: 0.7592 time to fit residues: 58.3453 Evaluate side-chains 78 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 372 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.084870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.069607 restraints weight = 13506.410| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.55 r_work: 0.2769 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8988 Z= 0.235 Angle : 0.642 7.987 12201 Z= 0.316 Chirality : 0.051 0.194 1353 Planarity : 0.005 0.035 1557 Dihedral : 11.849 166.663 1251 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.02 % Allowed : 8.20 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.26), residues: 1098 helix: 0.66 (0.25), residues: 465 sheet: 0.70 (0.37), residues: 201 loop : 1.48 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 183 TYR 0.010 0.001 TYR C 143 PHE 0.011 0.002 PHE A 262 TRP 0.014 0.003 TRP B 79 HIS 0.006 0.002 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 ( 8988) covalent geometry : angle 0.64216 / 0.32 (12201) hydrogen bonds : bond 0.04623 / 3.13 ( 447) hydrogen bonds : angle 4.74616 / 3.38 ( 1143) *********************** 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 85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8701 (pp) REVERT: A 314 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8565 (tp40) REVERT: A 328 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8482 (ttmp) REVERT: B 305 MET cc_start: 0.8984 (mmm) cc_final: 0.8712 (mmm) REVERT: B 355 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8271 (mtm) REVERT: C 82 MET cc_start: 0.9270 (tpt) cc_final: 0.8959 (tpt) REVERT: C 210 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8001 (ttm170) REVERT: C 227 MET cc_start: 0.8698 (mmm) cc_final: 0.8324 (mmm) REVERT: C 241 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: C 354 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7925 (tp40) REVERT: C 355 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8135 (mtp) REVERT: C 360 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7417 (tm-30) outliers start: 19 outliers final: 5 residues processed: 78 average time/residue: 0.7110 time to fit residues: 58.5104 Evaluate side-chains 77 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 106 optimal weight: 0.0040 chunk 47 optimal weight: 0.0170 chunk 7 optimal weight: 1.9990 overall best weight: 0.5632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.087271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.071972 restraints weight = 13333.474| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.58 r_work: 0.2814 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8988 Z= 0.103 Angle : 0.550 7.459 12201 Z= 0.261 Chirality : 0.044 0.171 1353 Planarity : 0.003 0.031 1557 Dihedral : 11.582 166.907 1251 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.17 % Allowed : 9.27 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.26), residues: 1098 helix: 0.98 (0.25), residues: 465 sheet: 0.69 (0.36), residues: 201 loop : 1.63 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.007 0.001 TYR C 69 PHE 0.008 0.001 PHE B 31 TRP 0.012 0.002 TRP C 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 8988) covalent geometry : angle 0.54963 / 0.26 (12201) hydrogen bonds : bond 0.03078 / 2.07 ( 447) hydrogen bonds : angle 4.44149 / 3.16 ( 1143) *********************** 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 77 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8659 (pp) REVERT: A 314 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8540 (tp40) REVERT: A 328 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8473 (ttmp) REVERT: B 305 MET cc_start: 0.9004 (mmm) cc_final: 0.8748 (mmm) REVERT: B 355 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8264 (mtm) REVERT: C 82 MET cc_start: 0.9219 (tpt) cc_final: 0.8894 (tpt) REVERT: C 227 MET cc_start: 0.8644 (mmm) cc_final: 0.8263 (mmm) REVERT: C 241 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: C 354 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7928 (tp40) REVERT: C 355 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8029 (mtp) REVERT: C 360 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7386 (tm-30) outliers start: 11 outliers final: 4 residues processed: 74 average time/residue: 0.8264 time to fit residues: 64.1488 Evaluate side-chains 76 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.071601 restraints weight = 13327.158| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.57 r_work: 0.2809 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8988 Z= 0.119 Angle : 0.560 7.335 12201 Z= 0.266 Chirality : 0.045 0.170 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.567 167.371 1251 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.38 % Allowed : 9.16 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.26), residues: 1098 helix: 1.00 (0.25), residues: 465 sheet: 0.70 (0.36), residues: 201 loop : 1.66 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.008 0.001 TYR C 143 PHE 0.009 0.001 PHE B 31 TRP 0.012 0.002 TRP B 79 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 8988) covalent geometry : angle 0.56000 / 0.27 (12201) hydrogen bonds : bond 0.03333 / 2.25 ( 447) hydrogen bonds : angle 4.43622 / 3.15 ( 1143) *********************** 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 78 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8666 (pp) REVERT: A 314 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8533 (tp40) REVERT: A 328 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8481 (ttmp) REVERT: B 305 MET cc_start: 0.9003 (mmm) cc_final: 0.8748 (mmm) REVERT: B 355 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8256 (mtm) REVERT: C 82 MET cc_start: 0.9223 (tpt) cc_final: 0.8999 (tpt) REVERT: C 227 MET cc_start: 0.8641 (mmm) cc_final: 0.8263 (mmm) REVERT: C 241 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: C 354 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7921 (tp40) REVERT: C 355 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8036 (mtp) REVERT: C 360 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7384 (tm-30) outliers start: 13 outliers final: 5 residues processed: 73 average time/residue: 0.8131 time to fit residues: 62.4678 Evaluate side-chains 76 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 0.0060 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.4554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.088312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.073082 restraints weight = 13368.066| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.59 r_work: 0.2839 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8988 Z= 0.091 Angle : 0.538 6.934 12201 Z= 0.252 Chirality : 0.044 0.151 1353 Planarity : 0.003 0.032 1557 Dihedral : 11.441 168.071 1251 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.06 % Allowed : 9.58 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.26), residues: 1098 helix: 1.15 (0.25), residues: 465 sheet: 0.78 (0.37), residues: 201 loop : 1.78 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.006 0.001 TYR B 143 PHE 0.007 0.001 PHE B 31 TRP 0.011 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 ( 8988) covalent geometry : angle 0.53795 / 0.25 (12201) hydrogen bonds : bond 0.02817 / 1.90 ( 447) hydrogen bonds : angle 4.30971 / 3.06 ( 1143) ********************** 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 76 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8645 (pp) REVERT: A 314 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8550 (tp40) REVERT: A 328 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8484 (ttmp) REVERT: B 305 MET cc_start: 0.8984 (mmm) cc_final: 0.8732 (mmm) REVERT: B 355 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8306 (mtm) REVERT: C 82 MET cc_start: 0.9201 (tpt) cc_final: 0.8948 (tpt) REVERT: C 227 MET cc_start: 0.8634 (mmm) cc_final: 0.8194 (mmm) REVERT: C 241 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: C 354 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7916 (tp40) REVERT: C 355 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.7995 (mtp) REVERT: C 360 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7412 (tm-30) outliers start: 10 outliers final: 4 residues processed: 72 average time/residue: 0.8175 time to fit residues: 61.7608 Evaluate side-chains 75 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 chunk 73 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.088021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.072792 restraints weight = 13147.239| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.57 r_work: 0.2831 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8988 Z= 0.099 Angle : 0.547 7.590 12201 Z= 0.256 Chirality : 0.044 0.155 1353 Planarity : 0.003 0.032 1557 Dihedral : 11.443 168.347 1251 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.17 % Allowed : 9.69 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.26), residues: 1098 helix: 1.18 (0.25), residues: 465 sheet: 0.78 (0.37), residues: 201 loop : 1.79 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.007 0.001 TYR B 143 PHE 0.008 0.001 PHE B 31 TRP 0.010 0.002 TRP B 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 8988) covalent geometry : angle 0.54708 / 0.26 (12201) hydrogen bonds : bond 0.02956 / 2.00 ( 447) hydrogen bonds : angle 4.31673 / 3.06 ( 1143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2877.96 seconds wall clock time: 49 minutes 53.91 seconds (2993.91 seconds total)