Starting phenix.real_space_refine on Fri Mar 14 02:03:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d14_27115/03_2025/8d14_27115.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d14_27115/03_2025/8d14_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d14_27115/03_2025/8d14_27115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d14_27115/03_2025/8d14_27115.map" model { file = "/net/cci-nas-00/data/ceres_data/8d14_27115/03_2025/8d14_27115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d14_27115/03_2025/8d14_27115.cif" } resolution = 2.51 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= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 8.22, per 1000 atoms: 0.89 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: 2.36 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: 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: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 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: 3.06 Time building geometry restraints manager: 2.77 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.680 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.590 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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= 0.275 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 (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: 1.45 (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 TRP 0.005 0.001 TRP C 340 HIS 0.002 0.001 HIS A 275 PHE 0.008 0.001 PHE A 255 TYR 0.010 0.001 TYR C 143 ARG 0.003 0.000 ARG C 210 *********************** 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 : 1.030 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: 0.6513 (mt-10) cc_final: 0.6276 (mm-30) outliers start: 3 outliers final: 0 residues processed: 109 average time/residue: 1.8531 time to fit residues: 211.9107 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 : 1.007 ------------------------------------------------------------------------------- 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: 4.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3148 r_free = 0.3148 target = 0.085407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.069926 restraints weight = 13337.325| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.58 r_work: 0.2770 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8988 Z= 0.367 Angle : 0.666 8.528 12201 Z= 0.333 Chirality : 0.052 0.208 1353 Planarity : 0.005 0.035 1557 Dihedral : 11.857 164.969 1251 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.38 % Allowed : 7.24 % 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: 1.34 (0.26), residues: 1098 helix: 0.61 (0.25), residues: 465 sheet: 0.64 (0.36), residues: 201 loop : 1.70 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 79 HIS 0.007 0.002 HIS C 371 PHE 0.015 0.002 PHE A 262 TYR 0.010 0.002 TYR C 143 ARG 0.008 0.001 ARG A 28 *********************** 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 : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7903 (p0) cc_final: 0.7578 (p0) REVERT: A 64 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8697 (pp) REVERT: A 82 MET cc_start: 0.9278 (tpt) cc_final: 0.9050 (tpt) REVERT: B 305 MET cc_start: 0.9024 (mmm) cc_final: 0.8800 (mmm) REVERT: B 355 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8289 (mmm) REVERT: C 47 MET cc_start: 0.6237 (pmm) cc_final: 0.5941 (pmm) REVERT: C 82 MET cc_start: 0.9263 (tpt) cc_final: 0.8985 (tpt) REVERT: C 227 MET cc_start: 0.8641 (mmm) cc_final: 0.8324 (mmm) REVERT: C 354 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.8020 (tp40) REVERT: C 355 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8226 (mtp) REVERT: C 360 GLN cc_start: 0.7799 (tm-30) cc_final: 0.6682 (tm-30) REVERT: C 364 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7102 (mt-10) outliers start: 13 outliers final: 5 residues processed: 76 average time/residue: 1.8665 time to fit residues: 149.6872 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 : 1.108 ------------------------------------------------------------------------------- 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 80 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3164 r_free = 0.3164 target = 0.086381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.070956 restraints weight = 13416.532| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.59 r_work: 0.2790 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8988 Z= 0.225 Angle : 0.583 7.912 12201 Z= 0.284 Chirality : 0.047 0.184 1353 Planarity : 0.004 0.033 1557 Dihedral : 11.673 165.943 1251 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.49 % Allowed : 7.77 % 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 (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: 1.43 (0.26), residues: 1098 helix: 0.73 (0.25), residues: 465 sheet: 0.81 (0.36), residues: 198 loop : 1.59 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 79 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE B 31 TYR 0.008 0.001 TYR C 143 ARG 0.006 0.001 ARG A 28 *********************** 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: 14 poor density : 67 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7780 (p0) cc_final: 0.7543 (p0) REVERT: A 314 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8527 (tp40) REVERT: B 123 MET cc_start: 0.9120 (mmp) cc_final: 0.8902 (tpt) REVERT: B 305 MET cc_start: 0.9033 (mmm) cc_final: 0.8798 (mmm) REVERT: B 355 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8272 (mtm) REVERT: C 82 MET cc_start: 0.9232 (tpt) cc_final: 0.8935 (tpt) REVERT: C 227 MET cc_start: 0.8670 (mmm) cc_final: 0.8319 (mmm) REVERT: C 241 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: C 354 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7997 (tp40) REVERT: C 355 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8189 (mtp) REVERT: C 360 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7510 (tm-30) outliers start: 14 outliers final: 7 residues processed: 75 average time/residue: 2.2151 time to fit residues: 175.6024 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 : 1.560 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN C 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.086000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.070710 restraints weight = 13210.130| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.57 r_work: 0.2787 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8988 Z= 0.231 Angle : 0.584 7.805 12201 Z= 0.283 Chirality : 0.047 0.183 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.672 166.584 1251 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.60 % Allowed : 8.09 % Favored : 90.31 % 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: 1.42 (0.26), residues: 1098 helix: 0.78 (0.25), residues: 465 sheet: 0.71 (0.37), residues: 201 loop : 1.59 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE C 255 TYR 0.009 0.001 TYR C 143 ARG 0.004 0.000 ARG A 28 *********************** 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 79 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8691 (pp) REVERT: A 314 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8523 (tp40) REVERT: A 328 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8413 (ttmp) REVERT: B 305 MET cc_start: 0.9011 (mmm) cc_final: 0.8765 (mmm) REVERT: B 355 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8300 (mtm) REVERT: C 82 MET cc_start: 0.9235 (tpt) cc_final: 0.9023 (tpt) REVERT: C 227 MET cc_start: 0.8661 (mmm) cc_final: 0.8295 (mmm) REVERT: C 353 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8206 (mp-120) REVERT: C 354 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7987 (tp40) REVERT: C 355 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8077 (mtp) REVERT: C 360 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7356 (tm-30) outliers start: 15 outliers final: 7 residues processed: 74 average time/residue: 2.1123 time to fit residues: 165.0288 Evaluate side-chains 77 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.220 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.085840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.070531 restraints weight = 13284.334| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.58 r_work: 0.2784 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8988 Z= 0.251 Angle : 0.589 7.826 12201 Z= 0.286 Chirality : 0.047 0.184 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.702 166.441 1251 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.81 % Allowed : 8.31 % 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 (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: 1.38 (0.26), residues: 1098 helix: 0.78 (0.25), residues: 465 sheet: 0.68 (0.37), residues: 201 loop : 1.53 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.005 0.001 HIS B 161 PHE 0.009 0.001 PHE B 31 TYR 0.009 0.001 TYR C 143 ARG 0.003 0.000 ARG A 28 *********************** 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 81 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8705 (pp) REVERT: A 314 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8536 (tp40) REVERT: A 328 LYS cc_start: 0.8755 (ttpp) cc_final: 0.8430 (ttmp) REVERT: B 305 MET cc_start: 0.9011 (mmm) cc_final: 0.8763 (mmm) REVERT: B 355 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8304 (mtm) REVERT: C 82 MET cc_start: 0.9240 (tpt) cc_final: 0.9027 (tpt) REVERT: C 227 MET cc_start: 0.8664 (mmm) cc_final: 0.8295 (mmm) REVERT: C 241 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: C 353 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7710 (mp-120) REVERT: C 354 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7917 (tp40) REVERT: C 355 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8083 (mtp) REVERT: C 360 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7364 (tm-30) outliers start: 17 outliers final: 7 residues processed: 75 average time/residue: 1.9910 time to fit residues: 157.0554 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 : 1.177 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 32 optimal weight: 0.0270 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.086513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.071290 restraints weight = 13067.982| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.56 r_work: 0.2799 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 : 0.003 0.032 8988 Z= 0.188 Angle : 0.564 7.627 12201 Z= 0.271 Chirality : 0.045 0.176 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.631 166.768 1251 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.70 % Allowed : 9.16 % 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 (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: 1.49 (0.26), residues: 1098 helix: 0.89 (0.25), residues: 465 sheet: 0.68 (0.37), residues: 201 loop : 1.57 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.004 0.001 HIS A 161 PHE 0.009 0.001 PHE B 31 TYR 0.008 0.001 TYR C 143 ARG 0.003 0.000 ARG A 28 *********************** 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: 16 poor density : 65 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8685 (pp) REVERT: A 314 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8516 (tp40) REVERT: A 328 LYS cc_start: 0.8747 (ttpp) cc_final: 0.8415 (ttmp) REVERT: B 305 MET cc_start: 0.9007 (mmm) cc_final: 0.8751 (mmm) REVERT: B 355 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8274 (mtm) REVERT: C 82 MET cc_start: 0.9228 (tpt) cc_final: 0.9013 (tpt) REVERT: C 227 MET cc_start: 0.8648 (mmm) cc_final: 0.8280 (mmm) REVERT: C 241 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: C 353 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7467 (mp-120) REVERT: C 354 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7907 (tp40) REVERT: C 355 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8094 (mtp) REVERT: C 360 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7364 (tm-30) outliers start: 16 outliers final: 7 residues processed: 74 average time/residue: 1.8264 time to fit residues: 142.2761 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 : 1.016 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 104 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.086574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.071260 restraints weight = 13415.162| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.58 r_work: 0.2798 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8988 Z= 0.192 Angle : 0.565 7.497 12201 Z= 0.271 Chirality : 0.046 0.174 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.615 167.010 1251 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.60 % Allowed : 9.16 % Favored : 89.24 % 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: 1.51 (0.26), residues: 1098 helix: 0.92 (0.25), residues: 465 sheet: 0.66 (0.37), residues: 201 loop : 1.59 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE B 31 TYR 0.008 0.001 TYR C 143 ARG 0.003 0.000 ARG A 28 *********************** 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 79 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8687 (pp) REVERT: A 314 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8531 (tp40) REVERT: A 328 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8420 (ttmp) REVERT: B 305 MET cc_start: 0.9008 (mmm) cc_final: 0.8752 (mmm) REVERT: B 355 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8301 (mtm) REVERT: C 82 MET cc_start: 0.9228 (tpt) cc_final: 0.9009 (tpt) REVERT: C 227 MET cc_start: 0.8668 (mmm) cc_final: 0.8291 (mmm) REVERT: C 241 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: C 354 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7899 (tp40) REVERT: C 355 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8145 (mtp) REVERT: C 360 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7371 (tm-30) outliers start: 15 outliers final: 8 residues processed: 72 average time/residue: 1.9275 time to fit residues: 146.2165 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 : 1.158 ------------------------------------------------------------------------------- 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 A residue 372 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3122 r_free = 0.3122 target = 0.083789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.068248 restraints weight = 13672.520| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.60 r_work: 0.2745 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 8988 Z= 0.501 Angle : 0.710 8.390 12201 Z= 0.354 Chirality : 0.055 0.206 1353 Planarity : 0.006 0.045 1557 Dihedral : 12.033 166.455 1251 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.81 % Allowed : 9.16 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.98 (0.26), residues: 1098 helix: 0.45 (0.24), residues: 462 sheet: 0.42 (0.36), residues: 207 loop : 1.34 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 79 HIS 0.007 0.002 HIS B 161 PHE 0.012 0.003 PHE A 262 TYR 0.011 0.002 TYR C 143 ARG 0.008 0.001 ARG C 183 *********************** 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 82 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8723 (pp) REVERT: A 314 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8582 (tp40) REVERT: A 328 LYS cc_start: 0.8840 (ttpp) cc_final: 0.8500 (ttmp) REVERT: B 305 MET cc_start: 0.8970 (mmm) cc_final: 0.8709 (mmm) REVERT: B 355 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8306 (mtm) REVERT: C 82 MET cc_start: 0.9274 (tpt) cc_final: 0.8978 (tpt) REVERT: C 227 MET cc_start: 0.8679 (mmm) cc_final: 0.8329 (mmm) REVERT: C 354 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7842 (tp40) REVERT: C 355 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8158 (mtp) REVERT: C 360 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7363 (tm-30) outliers start: 17 outliers final: 7 residues processed: 76 average time/residue: 1.9928 time to fit residues: 159.1155 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 : 1.004 ------------------------------------------------------------------------------- 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 45 VAL Chi-restraints excluded: chain C residue 72 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3176 r_free = 0.3176 target = 0.087038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.071786 restraints weight = 13244.277| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.57 r_work: 0.2810 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1902 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= 0.160 Angle : 0.560 7.626 12201 Z= 0.267 Chirality : 0.045 0.179 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.641 166.886 1251 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.75 % Allowed : 10.33 % Favored : 88.92 % 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: 1.38 (0.26), residues: 1098 helix: 0.86 (0.25), residues: 465 sheet: 0.54 (0.36), residues: 201 loop : 1.49 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE B 31 TYR 0.007 0.001 TYR B 69 ARG 0.003 0.000 ARG A 28 *********************** 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 75 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8675 (pp) REVERT: A 314 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8549 (tp40) REVERT: A 328 LYS cc_start: 0.8795 (ttpp) cc_final: 0.8466 (ttmp) REVERT: B 305 MET cc_start: 0.9006 (mmm) cc_final: 0.8756 (mmm) REVERT: B 355 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8222 (mtm) REVERT: C 47 MET cc_start: 0.6066 (ppp) cc_final: 0.5604 (ppp) REVERT: C 82 MET cc_start: 0.9218 (tpt) cc_final: 0.9013 (tpt) REVERT: C 227 MET cc_start: 0.8684 (mmm) cc_final: 0.8248 (mmm) REVERT: C 354 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7907 (tp40) REVERT: C 355 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8043 (mtp) REVERT: C 360 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7394 (tm-30) outliers start: 7 outliers final: 1 residues processed: 73 average time/residue: 1.8366 time to fit residues: 141.2013 Evaluate side-chains 71 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 B residue 355 MET 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 2 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 30 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.088036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.072851 restraints weight = 13374.407| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.58 r_work: 0.2832 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1887 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= 0.134 Angle : 0.540 7.012 12201 Z= 0.254 Chirality : 0.044 0.155 1353 Planarity : 0.003 0.033 1557 Dihedral : 11.486 168.971 1251 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.75 % Allowed : 10.54 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.26), residues: 1098 helix: 1.10 (0.25), residues: 465 sheet: 0.65 (0.36), residues: 201 loop : 1.74 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 PHE 0.008 0.001 PHE B 31 TYR 0.008 0.001 TYR C 69 ARG 0.003 0.000 ARG A 28 ********************** 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 73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8648 (pp) REVERT: A 314 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8519 (tp40) REVERT: A 328 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8480 (ttmp) REVERT: B 305 MET cc_start: 0.8987 (mmm) cc_final: 0.8644 (mmm) REVERT: B 355 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8310 (mtm) REVERT: C 82 MET cc_start: 0.9197 (tpt) cc_final: 0.8945 (tpt) REVERT: C 227 MET cc_start: 0.8631 (mmm) cc_final: 0.8202 (mmm) REVERT: C 354 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7906 (tp40) REVERT: C 355 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7970 (mtp) REVERT: C 360 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7414 (tm-30) outliers start: 7 outliers final: 1 residues processed: 71 average time/residue: 1.8723 time to fit residues: 140.0583 Evaluate side-chains 72 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 B residue 355 MET 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 6 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 100 optimal weight: 0.0870 chunk 81 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.3181 r_free = 0.3181 target = 0.087209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.072012 restraints weight = 13276.237| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.57 r_work: 0.2816 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1901 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= 0.171 Angle : 0.559 7.159 12201 Z= 0.265 Chirality : 0.045 0.165 1353 Planarity : 0.004 0.032 1557 Dihedral : 11.521 167.958 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 : 0.64 % Allowed : 10.44 % Favored : 88.92 % 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: 1.66 (0.26), residues: 1098 helix: 1.06 (0.25), residues: 465 sheet: 0.65 (0.36), residues: 201 loop : 1.70 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE B 31 TYR 0.008 0.001 TYR C 143 ARG 0.003 0.000 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7180.99 seconds wall clock time: 126 minutes 43.42 seconds (7603.42 seconds total)