Starting phenix.real_space_refine on Thu Feb 13 22:20:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d14_27115/02_2025/8d14_27115.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d14_27115/02_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_27115/02_2025/8d14_27115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d14_27115/02_2025/8d14_27115.map" model { file = "/net/cci-nas-00/data/ceres_data/8d14_27115/02_2025/8d14_27115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d14_27115/02_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-5592/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: 8.04, per 1000 atoms: 0.87 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 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: 1.32 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: 3.39 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.050 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: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 27.250 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.150 ------------------------------------------------------------------------------- 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 : 1.062 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: 1.8715 time to fit residues: 214.0469 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 : 1.001 ------------------------------------------------------------------------------- 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 = 0.085408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.069934 restraints weight = 13337.274| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.58 r_work: 0.2771 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 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 : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7906 (p0) cc_final: 0.7581 (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: 0.9049 (tpt) REVERT: B 305 MET cc_start: 0.9020 (mmm) cc_final: 0.8797 (mmm) REVERT: B 355 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8288 (mmm) REVERT: C 47 MET cc_start: 0.6239 (pmm) cc_final: 0.5943 (pmm) REVERT: C 82 MET cc_start: 0.9263 (tpt) cc_final: 0.8984 (tpt) REVERT: C 227 MET cc_start: 0.8637 (mmm) cc_final: 0.8319 (mmm) REVERT: C 354 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.8021 (tp40) REVERT: C 355 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8228 (mtp) REVERT: C 360 GLN cc_start: 0.7802 (tm-30) cc_final: 0.6688 (tm-30) REVERT: C 364 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7103 (mt-10) outliers start: 13 outliers final: 5 residues processed: 76 average time/residue: 1.8859 time to fit residues: 151.0296 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 : 1.007 ------------------------------------------------------------------------------- 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: 0.9990 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.086978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.071572 restraints weight = 13410.481| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.59 r_work: 0.2802 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1539 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= 0.187 Angle : 0.566 7.726 12201 Z= 0.274 Chirality : 0.046 0.181 1353 Planarity : 0.004 0.033 1557 Dihedral : 11.599 165.650 1251 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.38 % Allowed : 7.77 % Favored : 90.84 % 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: 1.50 (0.26), residues: 1098 helix: 0.80 (0.25), residues: 465 sheet: 0.71 (0.36), residues: 201 loop : 1.71 (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 C 161 PHE 0.008 0.001 PHE B 31 TYR 0.008 0.001 TYR C 143 ARG 0.006 0.000 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 80 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7788 (p0) cc_final: 0.7552 (p0) REVERT: A 314 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8540 (tp40) REVERT: B 305 MET cc_start: 0.9025 (mmm) cc_final: 0.8799 (mmm) REVERT: B 355 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8297 (mtm) REVERT: C 47 MET cc_start: 0.6293 (pmm) cc_final: 0.5890 (pmm) REVERT: C 82 MET cc_start: 0.9221 (tpt) cc_final: 0.8912 (tpt) REVERT: C 227 MET cc_start: 0.8647 (mmm) cc_final: 0.8293 (mmm) REVERT: C 241 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: C 354 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8041 (tp40) REVERT: C 355 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8189 (mtp) REVERT: C 360 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7521 (tm-30) outliers start: 13 outliers final: 5 residues processed: 75 average time/residue: 1.8524 time to fit residues: 146.2380 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 : 1.010 ------------------------------------------------------------------------------- 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 61 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3155 r_free = 0.3155 target = 0.085767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.070457 restraints weight = 13258.012| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.57 r_work: 0.2784 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1732 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= 0.255 Angle : 0.594 7.909 12201 Z= 0.289 Chirality : 0.048 0.187 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.701 166.572 1251 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.70 % Allowed : 7.77 % Favored : 90.52 % 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: 1.44 (0.26), residues: 1098 helix: 0.76 (0.25), residues: 465 sheet: 0.72 (0.37), residues: 201 loop : 1.62 (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 A 161 PHE 0.009 0.002 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 81 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8693 (pp) REVERT: A 314 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8549 (tp40) REVERT: A 328 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8400 (ttmp) REVERT: B 305 MET cc_start: 0.9020 (mmm) cc_final: 0.8778 (mmm) REVERT: B 355 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8320 (mtm) REVERT: C 82 MET cc_start: 0.9240 (tpt) cc_final: 0.8926 (tpt) REVERT: C 210 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8117 (ttm170) REVERT: C 227 MET cc_start: 0.8659 (mmm) cc_final: 0.8287 (mmm) REVERT: C 241 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: C 353 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8150 (mp-120) REVERT: C 354 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7990 (tp40) REVERT: C 355 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8072 (mtp) REVERT: C 360 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7348 (tm-30) outliers start: 16 outliers final: 6 residues processed: 76 average time/residue: 1.9176 time to fit residues: 153.3111 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 : 1.096 ------------------------------------------------------------------------------- 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 45 VAL 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 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: 1.9990 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3149 r_free = 0.3149 target = 0.085434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.070090 restraints weight = 13284.596| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.57 r_work: 0.2775 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8988 Z= 0.297 Angle : 0.611 8.001 12201 Z= 0.299 Chirality : 0.049 0.189 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.767 166.497 1251 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.70 % Allowed : 8.31 % Favored : 89.99 % 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: 1.32 (0.26), residues: 1098 helix: 0.69 (0.25), residues: 465 sheet: 0.67 (0.37), residues: 201 loop : 1.53 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 79 HIS 0.005 0.002 HIS B 161 PHE 0.010 0.002 PHE B 31 TYR 0.009 0.001 TYR C 143 ARG 0.004 0.001 ARG C 183 *********************** 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: 16 poor density : 64 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8714 (pp) REVERT: A 314 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8546 (tp40) REVERT: A 328 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8434 (ttmp) REVERT: B 305 MET cc_start: 0.8996 (mmm) cc_final: 0.8746 (mmm) REVERT: B 355 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8294 (mtm) REVERT: C 82 MET cc_start: 0.9251 (tpt) cc_final: 0.9029 (tpt) REVERT: C 210 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8122 (ttm170) REVERT: C 227 MET cc_start: 0.8679 (mmm) cc_final: 0.8326 (mmm) REVERT: C 241 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: C 354 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7919 (tp40) REVERT: C 355 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8208 (mtp) REVERT: C 360 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7385 (tm-30) outliers start: 16 outliers final: 6 residues processed: 75 average time/residue: 1.8893 time to fit residues: 149.1609 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 : 1.055 ------------------------------------------------------------------------------- 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 45 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 85 optimal weight: 0.0980 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.086942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.071712 restraints weight = 13055.426| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.56 r_work: 0.2807 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1799 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= 0.169 Angle : 0.554 7.513 12201 Z= 0.265 Chirality : 0.045 0.171 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.589 166.851 1251 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.60 % Allowed : 8.63 % 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 (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: 1.54 (0.26), residues: 1098 helix: 0.92 (0.25), residues: 465 sheet: 0.67 (0.37), residues: 201 loop : 1.66 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE B 31 TYR 0.007 0.001 TYR C 69 ARG 0.004 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 79 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8679 (pp) REVERT: A 314 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8520 (tp40) REVERT: A 328 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8424 (ttmp) REVERT: B 305 MET cc_start: 0.9011 (mmm) cc_final: 0.8752 (mmm) REVERT: B 355 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8261 (mtm) REVERT: C 82 MET cc_start: 0.9219 (tpt) cc_final: 0.8884 (tpt) REVERT: C 227 MET cc_start: 0.8641 (mmm) cc_final: 0.8280 (mmm) REVERT: C 354 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7966 (tp40) REVERT: C 355 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8086 (mtp) REVERT: C 360 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7363 (tm-30) outliers start: 15 outliers final: 6 residues processed: 72 average time/residue: 1.8871 time to fit residues: 143.1432 Evaluate side-chains 75 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 6.9990 chunk 88 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3152 r_free = 0.3152 target = 0.085587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.070211 restraints weight = 13459.828| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.59 r_work: 0.2778 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8988 Z= 0.267 Angle : 0.599 7.789 12201 Z= 0.291 Chirality : 0.048 0.183 1353 Planarity : 0.004 0.030 1557 Dihedral : 11.722 166.801 1251 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.49 % Allowed : 9.37 % 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: 1.38 (0.26), residues: 1098 helix: 0.78 (0.25), residues: 465 sheet: 0.61 (0.37), residues: 201 loop : 1.56 (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 0.002 PHE A 31 TYR 0.009 0.001 TYR C 143 ARG 0.003 0.000 ARG C 183 *********************** 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 78 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8710 (pp) REVERT: A 314 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8548 (tp40) REVERT: A 328 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8459 (ttmp) REVERT: B 305 MET cc_start: 0.9002 (mmm) cc_final: 0.8744 (mmm) REVERT: B 355 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8250 (mtm) REVERT: C 82 MET cc_start: 0.9240 (tpt) cc_final: 0.9025 (tpt) REVERT: C 210 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8117 (ttm170) REVERT: C 227 MET cc_start: 0.8676 (mmm) cc_final: 0.8308 (mmm) REVERT: C 241 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: C 354 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7935 (tp40) REVERT: C 355 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8059 (mtp) REVERT: C 360 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7419 (tm-30) outliers start: 14 outliers final: 5 residues processed: 74 average time/residue: 1.9721 time to fit residues: 153.6942 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 : 1.193 ------------------------------------------------------------------------------- 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 34 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3137 r_free = 0.3137 target = 0.084684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.069174 restraints weight = 13621.068| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.60 r_work: 0.2764 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8988 Z= 0.341 Angle : 0.638 8.125 12201 Z= 0.313 Chirality : 0.050 0.195 1353 Planarity : 0.005 0.034 1557 Dihedral : 11.884 166.468 1251 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.38 % Allowed : 9.69 % 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: 1.18 (0.26), residues: 1098 helix: 0.63 (0.25), residues: 465 sheet: 0.50 (0.36), residues: 201 loop : 1.43 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 79 HIS 0.006 0.002 HIS B 161 PHE 0.010 0.002 PHE A 31 TYR 0.010 0.001 TYR C 143 ARG 0.004 0.000 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 79 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8684 (pp) REVERT: A 314 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8540 (tp40) REVERT: A 328 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8472 (ttmp) REVERT: B 305 MET cc_start: 0.8979 (mmm) cc_final: 0.8721 (mmm) REVERT: B 355 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8308 (mtm) REVERT: C 47 MET cc_start: 0.6083 (ppp) cc_final: 0.5630 (ppp) REVERT: C 82 MET cc_start: 0.9262 (tpt) cc_final: 0.8952 (tpt) REVERT: C 210 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8101 (ttm170) REVERT: C 227 MET cc_start: 0.8689 (mmm) cc_final: 0.8251 (mmm) REVERT: C 354 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7893 (tp40) REVERT: C 355 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8035 (mtp) REVERT: C 360 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7410 (tm-30) outliers start: 13 outliers final: 5 residues processed: 75 average time/residue: 1.9413 time to fit residues: 153.2051 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 : 1.129 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 90 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 14 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3178 r_free = 0.3178 target = 0.087125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.071840 restraints weight = 13242.409| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.57 r_work: 0.2811 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1893 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= 0.154 Angle : 0.554 7.537 12201 Z= 0.264 Chirality : 0.045 0.171 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.613 167.026 1251 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.49 % Allowed : 9.58 % 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: 1.49 (0.26), residues: 1098 helix: 0.92 (0.25), residues: 465 sheet: 0.53 (0.36), residues: 201 loop : 1.63 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.003 0.001 HIS C 161 PHE 0.009 0.001 PHE B 31 TYR 0.007 0.001 TYR C 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 81 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8675 (pp) REVERT: A 314 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8534 (tp40) REVERT: A 328 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8467 (ttmp) REVERT: B 305 MET cc_start: 0.9006 (mmm) cc_final: 0.8758 (mmm) REVERT: B 355 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8287 (mtm) REVERT: C 47 MET cc_start: 0.6164 (ppp) cc_final: 0.5701 (ppp) REVERT: C 82 MET cc_start: 0.9217 (tpt) cc_final: 0.9004 (tpt) REVERT: C 227 MET cc_start: 0.8677 (mmm) cc_final: 0.8231 (mmm) REVERT: C 354 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7908 (tp40) REVERT: C 355 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8024 (mtp) REVERT: C 360 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7382 (tm-30) outliers start: 14 outliers final: 7 residues processed: 76 average time/residue: 1.9428 time to fit residues: 155.2548 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 : 1.077 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 6 optimal weight: 0.0020 chunk 30 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.3183 r_free = 0.3183 target = 0.087276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.072001 restraints weight = 13394.527| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.58 r_work: 0.2816 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1892 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= 0.154 Angle : 0.550 7.192 12201 Z= 0.260 Chirality : 0.044 0.162 1353 Planarity : 0.004 0.032 1557 Dihedral : 11.531 167.920 1251 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.17 % Allowed : 9.90 % 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: 1.65 (0.26), residues: 1098 helix: 1.03 (0.25), residues: 465 sheet: 0.62 (0.36), residues: 201 loop : 1.74 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.003 0.001 HIS A 161 PHE 0.008 0.001 PHE B 31 TYR 0.007 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 76 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8670 (pp) REVERT: A 314 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8548 (tp40) REVERT: A 328 LYS cc_start: 0.8758 (ttpp) cc_final: 0.8456 (ttmp) REVERT: B 305 MET cc_start: 0.8996 (mmm) cc_final: 0.8652 (mmm) REVERT: B 355 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8287 (mtm) REVERT: C 47 MET cc_start: 0.6134 (ppp) cc_final: 0.5655 (ppp) REVERT: C 82 MET cc_start: 0.9208 (tpt) cc_final: 0.8964 (tpt) REVERT: C 227 MET cc_start: 0.8649 (mmm) cc_final: 0.8282 (mmm) REVERT: C 354 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7904 (tp40) REVERT: C 355 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7979 (mtp) REVERT: C 360 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7400 (tm-30) outliers start: 11 outliers final: 6 residues processed: 71 average time/residue: 2.0251 time to fit residues: 151.3609 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 : 1.215 ------------------------------------------------------------------------------- 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 A residue 355 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 100 optimal weight: 0.0270 chunk 81 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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 = 0.3172 r_free = 0.3172 target = 0.086744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.071506 restraints weight = 13272.338| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.57 r_work: 0.2806 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1918 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= 0.187 Angle : 0.562 7.271 12201 Z= 0.269 Chirality : 0.045 0.171 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.576 167.710 1251 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.28 % Allowed : 9.90 % Favored : 88.82 % 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: 1.58 (0.26), residues: 1098 helix: 0.98 (0.25), residues: 465 sheet: 0.59 (0.36), residues: 201 loop : 1.68 (0.32), 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6525.18 seconds wall clock time: 116 minutes 20.77 seconds (6980.77 seconds total)