Starting phenix.real_space_refine on Sun Dec 29 00:44:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d14_27115/12_2024/8d14_27115.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d14_27115/12_2024/8d14_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_27115/12_2024/8d14_27115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d14_27115/12_2024/8d14_27115.map" model { file = "/net/cci-nas-00/data/ceres_data/8d14_27115/12_2024/8d14_27115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d14_27115/12_2024/8d14_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.37, per 1000 atoms: 0.91 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: 2.51 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: 1.54 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: 3.11 Time building geometry restraints manager: 2.68 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.750 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.040 ------------------------------------------------------------------------------- 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 : 1.076 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: 1.8981 time to fit residues: 217.5718 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 : 1.294 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8851 (pp) REVERT: A 82 MET cc_start: 0.9122 (tpt) cc_final: 0.8844 (tpt) REVERT: B 305 MET cc_start: 0.8371 (mmm) cc_final: 0.8130 (mmm) REVERT: B 355 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7326 (mmm) REVERT: C 47 MET cc_start: 0.6348 (pmm) cc_final: 0.6118 (pmm) REVERT: C 82 MET cc_start: 0.9037 (tpt) cc_final: 0.8782 (tpt) REVERT: C 227 MET cc_start: 0.8566 (mmm) cc_final: 0.8280 (mmm) REVERT: C 354 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7494 (tp40) REVERT: C 355 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7253 (mtp) REVERT: C 360 GLN cc_start: 0.7241 (tm-30) cc_final: 0.6281 (tm-30) outliers start: 13 outliers final: 5 residues processed: 76 average time/residue: 1.8822 time to fit residues: 150.4315 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 : 1.085 ------------------------------------------------------------------------------- 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 56 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1511 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 : 0.561 7.712 12201 Z= 0.270 Chirality : 0.045 0.179 1353 Planarity : 0.004 0.033 1557 Dihedral : 11.594 165.532 1251 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.38 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: 1.53 (0.26), residues: 1098 helix: 0.81 (0.25), residues: 465 sheet: 0.73 (0.36), residues: 201 loop : 1.73 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.003 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 82 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: B 305 MET cc_start: 0.8371 (mmm) cc_final: 0.8017 (mmm) REVERT: B 355 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7300 (mtm) REVERT: C 47 MET cc_start: 0.6458 (pmm) cc_final: 0.6083 (pmm) REVERT: C 82 MET cc_start: 0.8989 (tpt) cc_final: 0.8708 (tpt) REVERT: C 227 MET cc_start: 0.8546 (mmm) cc_final: 0.8169 (mmm) REVERT: C 241 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: C 354 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7524 (tp40) REVERT: C 355 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7121 (mtp) REVERT: C 364 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6481 (mt-10) outliers start: 13 outliers final: 5 residues processed: 77 average time/residue: 1.9330 time to fit residues: 156.4521 Evaluate side-chains 73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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 75 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1707 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= 0.252 Angle : 0.598 7.871 12201 Z= 0.292 Chirality : 0.048 0.187 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.700 166.452 1251 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.70 % Allowed : 8.09 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.26), residues: 1098 helix: 0.78 (0.25), residues: 465 sheet: 0.73 (0.37), residues: 201 loop : 1.64 (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 82 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8845 (pp) REVERT: B 305 MET cc_start: 0.8378 (mmm) cc_final: 0.8119 (mmm) REVERT: B 355 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7261 (mtm) REVERT: C 82 MET cc_start: 0.9019 (tpt) cc_final: 0.8727 (tpt) REVERT: C 210 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8239 (ttm170) REVERT: C 227 MET cc_start: 0.8568 (mmm) cc_final: 0.8242 (mmm) REVERT: C 241 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: C 353 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8297 (mp-120) REVERT: C 354 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7467 (tp40) REVERT: C 355 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7151 (mtp) outliers start: 16 outliers final: 6 residues processed: 77 average time/residue: 1.9709 time to fit residues: 159.9983 Evaluate side-chains 75 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8988 Z= 0.407 Angle : 0.666 8.332 12201 Z= 0.331 Chirality : 0.052 0.199 1353 Planarity : 0.005 0.037 1557 Dihedral : 11.911 166.175 1251 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.02 % Allowed : 8.31 % Favored : 89.67 % 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: 1.15 (0.26), residues: 1098 helix: 0.58 (0.25), residues: 462 sheet: 0.50 (0.36), residues: 207 loop : 1.46 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 79 HIS 0.006 0.002 HIS B 161 PHE 0.011 0.002 PHE A 262 TYR 0.010 0.001 TYR C 143 ARG 0.006 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 82 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8851 (pp) REVERT: A 95 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6759 (mmm160) REVERT: B 305 MET cc_start: 0.8315 (mmm) cc_final: 0.8053 (mmm) REVERT: B 355 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7285 (mtm) REVERT: C 82 MET cc_start: 0.9050 (tpt) cc_final: 0.8747 (tpt) REVERT: C 210 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8000 (ttm170) REVERT: C 227 MET cc_start: 0.8610 (mmm) cc_final: 0.8222 (mmm) REVERT: C 241 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: C 353 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8183 (mp-120) REVERT: C 354 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7400 (tp40) REVERT: C 355 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7160 (mtp) outliers start: 19 outliers final: 6 residues processed: 75 average time/residue: 1.9244 time to fit residues: 152.2068 Evaluate side-chains 76 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 95 ARG 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8988 Z= 0.192 Angle : 0.572 7.857 12201 Z= 0.276 Chirality : 0.046 0.184 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.697 166.554 1251 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.38 % Allowed : 9.37 % 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: 1.38 (0.26), residues: 1098 helix: 0.80 (0.25), residues: 465 sheet: 0.63 (0.36), 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 0.004 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 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 75 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8839 (pp) REVERT: B 305 MET cc_start: 0.8342 (mmm) cc_final: 0.8073 (mmm) REVERT: B 355 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7260 (mtm) REVERT: C 47 MET cc_start: 0.6481 (ppp) cc_final: 0.6218 (ppp) REVERT: C 227 MET cc_start: 0.8592 (mmm) cc_final: 0.8208 (mmm) REVERT: C 353 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7897 (mp-120) REVERT: C 354 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7357 (tp40) REVERT: C 355 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7113 (mtp) outliers start: 13 outliers final: 6 residues processed: 69 average time/residue: 1.9314 time to fit residues: 140.3706 Evaluate side-chains 73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 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 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1829 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= 0.163 Angle : 0.555 7.518 12201 Z= 0.266 Chirality : 0.045 0.172 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.599 167.117 1251 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: 1.53 (0.26), residues: 1098 helix: 0.93 (0.25), residues: 465 sheet: 0.66 (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 B 161 PHE 0.009 0.001 PHE B 31 TYR 0.007 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 76 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8833 (pp) REVERT: B 305 MET cc_start: 0.8360 (mmm) cc_final: 0.8086 (mmm) REVERT: B 355 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7251 (mtm) REVERT: C 47 MET cc_start: 0.6439 (ppp) cc_final: 0.6197 (ppp) REVERT: C 227 MET cc_start: 0.8575 (mmm) cc_final: 0.8183 (mmm) REVERT: C 241 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: C 353 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7650 (mp-120) REVERT: C 354 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7357 (tp40) REVERT: C 355 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7130 (mtp) outliers start: 14 outliers final: 7 residues processed: 70 average time/residue: 1.9586 time to fit residues: 144.3099 Evaluate side-chains 75 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.0870 chunk 84 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8988 Z= 0.162 Angle : 0.552 7.336 12201 Z= 0.263 Chirality : 0.045 0.166 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.557 167.389 1251 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.49 % Allowed : 9.69 % 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: 1.59 (0.26), residues: 1098 helix: 0.98 (0.25), residues: 465 sheet: 0.68 (0.36), residues: 201 loop : 1.66 (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 0.007 0.001 TYR C 143 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8832 (pp) REVERT: B 305 MET cc_start: 0.8356 (mmm) cc_final: 0.8082 (mmm) REVERT: B 355 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7266 (mtm) REVERT: C 47 MET cc_start: 0.6509 (ppp) cc_final: 0.6253 (ppp) REVERT: C 227 MET cc_start: 0.8562 (mmm) cc_final: 0.8247 (mmm) REVERT: C 241 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: C 354 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7359 (tp40) REVERT: C 355 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7144 (mtp) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 1.9642 time to fit residues: 148.9181 Evaluate side-chains 73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1862 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= 0.177 Angle : 0.558 7.274 12201 Z= 0.266 Chirality : 0.045 0.169 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.561 167.596 1251 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.28 % Allowed : 10.22 % Favored : 88.50 % 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: 1.61 (0.26), residues: 1098 helix: 0.97 (0.25), residues: 465 sheet: 0.70 (0.37), 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 *********************** 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 74 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8830 (pp) REVERT: B 305 MET cc_start: 0.8367 (mmm) cc_final: 0.8094 (mmm) REVERT: B 355 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7270 (mtm) REVERT: C 47 MET cc_start: 0.6520 (ppp) cc_final: 0.6295 (ppp) REVERT: C 227 MET cc_start: 0.8560 (mmm) cc_final: 0.8236 (mmm) REVERT: C 241 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: C 354 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7363 (tp40) REVERT: C 355 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7108 (mtp) outliers start: 12 outliers final: 6 residues processed: 68 average time/residue: 2.0048 time to fit residues: 143.3439 Evaluate side-chains 73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8988 Z= 0.226 Angle : 0.584 7.525 12201 Z= 0.280 Chirality : 0.046 0.177 1353 Planarity : 0.004 0.030 1557 Dihedral : 11.648 167.291 1251 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.28 % Allowed : 10.33 % Favored : 88.39 % 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: 0.89 (0.25), residues: 465 sheet: 0.66 (0.36), residues: 201 loop : 1.65 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE B 31 TYR 0.009 0.001 TYR C 143 ARG 0.002 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 74 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8841 (pp) REVERT: A 314 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8113 (tp40) REVERT: B 305 MET cc_start: 0.8351 (mmm) cc_final: 0.8069 (mmm) REVERT: B 355 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7237 (mtm) REVERT: C 47 MET cc_start: 0.6547 (ppp) cc_final: 0.6341 (ppp) REVERT: C 227 MET cc_start: 0.8572 (mmm) cc_final: 0.8233 (mmm) REVERT: C 241 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: C 354 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7412 (tp40) REVERT: C 355 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7089 (mtp) outliers start: 12 outliers final: 5 residues processed: 70 average time/residue: 2.0130 time to fit residues: 148.5042 Evaluate side-chains 73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.0070 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3179 r_free = 0.3179 target = 0.087101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.071833 restraints weight = 13175.566| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.57 r_work: 0.2814 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1882 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= 0.165 Angle : 0.559 7.541 12201 Z= 0.265 Chirality : 0.045 0.167 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.553 167.541 1251 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.28 % Allowed : 10.44 % Favored : 88.29 % 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: 1.00 (0.25), residues: 465 sheet: 0.69 (0.37), residues: 201 loop : 1.74 (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 A 161 PHE 0.008 0.001 PHE B 31 TYR 0.007 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: 3553.82 seconds wall clock time: 65 minutes 49.71 seconds (3949.71 seconds total)