Starting phenix.real_space_refine on Fri Sep 27 02:49:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5onv_3835/09_2024/5onv_3835.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5onv_3835/09_2024/5onv_3835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5onv_3835/09_2024/5onv_3835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5onv_3835/09_2024/5onv_3835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5onv_3835/09_2024/5onv_3835.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5onv_3835/09_2024/5onv_3835.cif" } resolution = 4.1 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= 0.013 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 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9235 2.51 5 N 2470 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14640 Number of models: 1 Model: "" Number of chains: 2 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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, E, D Time building chain proxies: 6.03, per 1000 atoms: 0.41 Number of scatterers: 14640 At special positions: 0 Unit cell: (98.04, 85.5, 192.66, 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 105 16.00 P 10 15.00 Mg 5 11.99 O 2815 8.00 N 2470 7.00 C 9235 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: 3.57 Conformation dependent library (CDL) restraints added in 1.9 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 25 sheets defined 52.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 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 286 through 295 removed outlier: 4.685A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (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 349 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 181 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 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 286 through 295 removed outlier: 4.686A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (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 349 Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 181 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 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 286 through 295 removed outlier: 4.686A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (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 349 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 181 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.684A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 181 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 295 removed outlier: 4.685A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.926A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.434A 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 176 through 178 Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.926A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.926A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.925A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 176 through 178 Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.925A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'E' and resid 176 through 178 Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 780 hydrogen bonds defined for protein. 2025 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: 5.20 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3568 1.33 - 1.45: 3352 1.45 - 1.57: 7844 1.57 - 1.69: 11 1.69 - 1.81: 185 Bond restraints: 14960 Sorted by residual: bond pdb=" CA ILE B 151 " pdb=" C ILE B 151 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" CA ILE A 151 " pdb=" C ILE A 151 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.21e-02 6.83e+03 1.14e+01 bond pdb=" CA ILE E 151 " pdb=" C ILE E 151 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.21e-02 6.83e+03 1.13e+01 bond pdb=" CA ILE D 151 " pdb=" C ILE D 151 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.21e-02 6.83e+03 1.12e+01 bond pdb=" CA ILE C 151 " pdb=" C ILE C 151 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.21e-02 6.83e+03 1.11e+01 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 18932 2.76 - 5.52: 1197 5.52 - 8.27: 114 8.27 - 11.03: 47 11.03 - 13.79: 15 Bond angle restraints: 20305 Sorted by residual: angle pdb=" C VAL B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta sigma weight residual 119.24 127.99 -8.75 1.04e+00 9.25e-01 7.08e+01 angle pdb=" C VAL E 129 " pdb=" N PRO E 130 " pdb=" CA PRO E 130 " ideal model delta sigma weight residual 119.24 127.98 -8.74 1.04e+00 9.25e-01 7.06e+01 angle pdb=" C VAL D 129 " pdb=" N PRO D 130 " pdb=" CA PRO D 130 " ideal model delta sigma weight residual 119.24 127.95 -8.71 1.04e+00 9.25e-01 7.01e+01 angle pdb=" C VAL A 129 " pdb=" N PRO A 130 " pdb=" CA PRO A 130 " ideal model delta sigma weight residual 119.24 127.95 -8.71 1.04e+00 9.25e-01 7.01e+01 angle pdb=" C VAL C 129 " pdb=" N PRO C 130 " pdb=" CA PRO C 130 " ideal model delta sigma weight residual 119.24 127.94 -8.70 1.04e+00 9.25e-01 7.00e+01 ... (remaining 20300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 8735 24.98 - 49.97: 195 49.97 - 74.95: 55 74.95 - 99.94: 5 99.94 - 124.92: 5 Dihedral angle restraints: 8995 sinusoidal: 3635 harmonic: 5360 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.92 -124.92 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.92 -124.91 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.91 -124.91 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1159 0.047 - 0.093: 794 0.093 - 0.139: 229 0.139 - 0.186: 68 0.186 - 0.232: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA PRO E 32 " pdb=" N PRO E 32 " pdb=" C PRO E 32 " pdb=" CB PRO E 32 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO A 32 " pdb=" N PRO A 32 " pdb=" C PRO A 32 " pdb=" CB PRO A 32 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO B 32 " pdb=" N PRO B 32 " pdb=" C PRO B 32 " pdb=" CB PRO B 32 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2252 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 375 " -0.031 2.00e-02 2.50e+03 6.30e-02 3.97e+01 pdb=" C PHE A 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE A 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE A 375 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 375 " -0.031 2.00e-02 2.50e+03 6.30e-02 3.96e+01 pdb=" C PHE C 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE C 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE C 375 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 375 " -0.031 2.00e-02 2.50e+03 6.30e-02 3.96e+01 pdb=" C PHE D 375 " 0.109 2.00e-02 2.50e+03 pdb=" O PHE D 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE D 375 " -0.039 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 73 2.58 - 3.16: 13822 3.16 - 3.74: 23147 3.74 - 4.32: 35259 4.32 - 4.90: 53364 Nonbonded interactions: 125665 Sorted by model distance: nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.996 2.170 ... (remaining 125660 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' selection = chain 'D' selection = chain 'E' } 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 group one per residue 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: 0.960 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 31.910 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.013 0.059 14960 Z= 0.863 Angle : 1.559 13.788 20305 Z= 1.007 Chirality : 0.065 0.232 2255 Planarity : 0.018 0.148 2595 Dihedral : 11.903 124.921 5565 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 3.55 % Allowed : 6.28 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.18), residues: 1830 helix: -1.67 (0.14), residues: 840 sheet: -1.16 (0.29), residues: 325 loop : -1.83 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.008 TRP C 340 HIS 0.007 0.002 HIS B 88 PHE 0.024 0.004 PHE D 375 TYR 0.048 0.006 TYR C 306 ARG 0.004 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 729 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.6781 (m-30) cc_final: 0.6243 (t0) REVERT: A 34 ILE cc_start: 0.9600 (mt) cc_final: 0.9174 (tp) REVERT: A 78 ASN cc_start: 0.8024 (t0) cc_final: 0.6174 (t0) REVERT: A 81 ASP cc_start: 0.8614 (m-30) cc_final: 0.7840 (m-30) REVERT: A 86 TRP cc_start: 0.9000 (m-10) cc_final: 0.8461 (m-10) REVERT: A 101 HIS cc_start: 0.8657 (p-80) cc_final: 0.8381 (p-80) REVERT: A 103 THR cc_start: 0.9150 (m) cc_final: 0.8925 (t) REVERT: A 205 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7332 (mt-10) REVERT: A 212 ILE cc_start: 0.9101 (mt) cc_final: 0.8797 (mt) REVERT: A 217 CYS cc_start: 0.8849 (m) cc_final: 0.8635 (m) REVERT: A 287 ILE cc_start: 0.8526 (pt) cc_final: 0.8218 (tt) REVERT: A 291 LYS cc_start: 0.8939 (tmmt) cc_final: 0.8397 (mptt) REVERT: B 39 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7328 (ttp-170) REVERT: B 153 LEU cc_start: 0.9277 (tp) cc_final: 0.8853 (mt) REVERT: B 192 ILE cc_start: 0.8894 (pt) cc_final: 0.8644 (mm) REVERT: B 280 ASN cc_start: 0.8454 (m-40) cc_final: 0.8099 (m-40) REVERT: B 305 MET cc_start: 0.9134 (mmm) cc_final: 0.8280 (mmt) REVERT: B 352 PHE cc_start: 0.8985 (t80) cc_final: 0.8538 (t80) REVERT: B 370 VAL cc_start: 0.9205 (t) cc_final: 0.8988 (t) REVERT: C 21 PHE cc_start: 0.6982 (m-80) cc_final: 0.6700 (m-80) REVERT: C 47 MET cc_start: 0.5790 (mtm) cc_final: 0.5477 (ptp) REVERT: C 78 ASN cc_start: 0.7367 (t0) cc_final: 0.5630 (t0) REVERT: C 81 ASP cc_start: 0.8543 (m-30) cc_final: 0.7808 (m-30) REVERT: C 87 HIS cc_start: 0.8818 (t70) cc_final: 0.8513 (t-170) REVERT: C 157 ASP cc_start: 0.6669 (t70) cc_final: 0.6112 (t0) REVERT: C 161 HIS cc_start: 0.9368 (p90) cc_final: 0.9014 (p90) REVERT: C 165 ILE cc_start: 0.9235 (mt) cc_final: 0.8852 (tp) REVERT: C 176 MET cc_start: 0.7815 (mtt) cc_final: 0.7500 (mtp) REVERT: C 227 MET cc_start: 0.8793 (tmm) cc_final: 0.8510 (tmm) REVERT: C 267 ILE cc_start: 0.9221 (pt) cc_final: 0.8945 (mp) REVERT: C 280 ASN cc_start: 0.8636 (m-40) cc_final: 0.8430 (m-40) REVERT: C 292 ASP cc_start: 0.8383 (m-30) cc_final: 0.7877 (t0) REVERT: C 305 MET cc_start: 0.8730 (mmm) cc_final: 0.8482 (mmt) REVERT: C 340 TRP cc_start: 0.9034 (t60) cc_final: 0.8514 (t60) REVERT: D 43 VAL cc_start: 0.8558 (t) cc_final: 0.7246 (t) REVERT: D 47 MET cc_start: 0.6272 (mtm) cc_final: 0.5204 (ptp) REVERT: D 106 THR cc_start: 0.7793 (t) cc_final: 0.7508 (t) REVERT: D 127 PHE cc_start: 0.8855 (m-80) cc_final: 0.8611 (m-10) REVERT: D 137 GLN cc_start: 0.8093 (mt0) cc_final: 0.7370 (mm-40) REVERT: D 142 LEU cc_start: 0.9277 (mt) cc_final: 0.8956 (mt) REVERT: D 155 SER cc_start: 0.8418 (t) cc_final: 0.8208 (t) REVERT: D 157 ASP cc_start: 0.6757 (t70) cc_final: 0.6545 (t70) REVERT: D 162 ASN cc_start: 0.8722 (t0) cc_final: 0.8289 (p0) REVERT: D 165 ILE cc_start: 0.9133 (mt) cc_final: 0.8684 (tp) REVERT: D 214 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7863 (mt-10) REVERT: D 244 ASP cc_start: 0.9017 (p0) cc_final: 0.8808 (p0) REVERT: D 270 GLU cc_start: 0.7542 (tt0) cc_final: 0.7239 (pt0) REVERT: D 280 ASN cc_start: 0.9029 (m-40) cc_final: 0.7994 (m-40) REVERT: D 288 ASP cc_start: 0.7521 (t70) cc_final: 0.7138 (t0) REVERT: D 299 MET cc_start: 0.8340 (mtp) cc_final: 0.8128 (mtt) REVERT: D 305 MET cc_start: 0.8509 (mmm) cc_final: 0.8294 (tpp) REVERT: D 311 ASP cc_start: 0.8585 (m-30) cc_final: 0.8127 (t70) REVERT: D 358 THR cc_start: 0.8877 (p) cc_final: 0.8601 (t) REVERT: E 11 ASP cc_start: 0.8631 (t0) cc_final: 0.8362 (t0) REVERT: E 21 PHE cc_start: 0.7218 (m-80) cc_final: 0.6828 (m-80) REVERT: E 30 VAL cc_start: 0.9277 (t) cc_final: 0.9027 (m) REVERT: E 43 VAL cc_start: 0.8529 (t) cc_final: 0.7361 (t) REVERT: E 47 MET cc_start: 0.6952 (mtm) cc_final: 0.5809 (ttt) REVERT: E 78 ASN cc_start: 0.8135 (t0) cc_final: 0.7279 (t0) REVERT: E 87 HIS cc_start: 0.8871 (t70) cc_final: 0.8635 (t-170) REVERT: E 104 LEU cc_start: 0.9137 (tp) cc_final: 0.8876 (tp) REVERT: E 137 GLN cc_start: 0.8192 (mt0) cc_final: 0.7966 (mm-40) REVERT: E 205 GLU cc_start: 0.7870 (mt-10) cc_final: 0.6965 (mt-10) REVERT: E 211 ASP cc_start: 0.7563 (t70) cc_final: 0.7012 (t70) REVERT: E 280 ASN cc_start: 0.9023 (m-40) cc_final: 0.7977 (m110) REVERT: E 292 ASP cc_start: 0.8502 (m-30) cc_final: 0.8093 (t70) outliers start: 0 outliers final: 0 residues processed: 729 average time/residue: 0.2737 time to fit residues: 287.2308 Evaluate side-chains 372 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 263 GLN A 280 ASN B 87 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS C 40 HIS C 87 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14960 Z= 0.262 Angle : 0.735 7.373 20305 Z= 0.380 Chirality : 0.047 0.168 2255 Planarity : 0.007 0.054 2595 Dihedral : 7.209 86.824 2085 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.97 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 1830 helix: 0.22 (0.17), residues: 820 sheet: -0.75 (0.29), residues: 330 loop : -1.23 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 86 HIS 0.011 0.002 HIS C 275 PHE 0.016 0.001 PHE E 255 TYR 0.021 0.002 TYR C 166 ARG 0.006 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7259 (m-30) cc_final: 0.6561 (t70) REVERT: A 34 ILE cc_start: 0.9585 (mt) cc_final: 0.9339 (tp) REVERT: A 41 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 43 VAL cc_start: 0.8373 (t) cc_final: 0.8143 (t) REVERT: A 47 MET cc_start: 0.5195 (ptt) cc_final: 0.4987 (ptt) REVERT: A 118 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8938 (mmtt) REVERT: A 154 ASP cc_start: 0.8299 (t70) cc_final: 0.7788 (t70) REVERT: A 217 CYS cc_start: 0.8725 (m) cc_final: 0.8417 (m) REVERT: A 345 ILE cc_start: 0.9693 (mt) cc_final: 0.9488 (mm) REVERT: B 41 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7522 (tm-30) REVERT: B 47 MET cc_start: 0.5810 (mtm) cc_final: 0.4767 (tpp) REVERT: B 105 LEU cc_start: 0.9442 (mp) cc_final: 0.9143 (mp) REVERT: B 106 THR cc_start: 0.8759 (t) cc_final: 0.8506 (p) REVERT: B 117 GLU cc_start: 0.8623 (pt0) cc_final: 0.8369 (pp20) REVERT: B 123 MET cc_start: 0.8543 (mmp) cc_final: 0.7842 (mmp) REVERT: B 153 LEU cc_start: 0.9202 (tp) cc_final: 0.8649 (mt) REVERT: B 192 ILE cc_start: 0.8924 (pt) cc_final: 0.8626 (pt) REVERT: B 252 ASN cc_start: 0.9313 (p0) cc_final: 0.9111 (p0) REVERT: B 253 GLU cc_start: 0.8306 (mp0) cc_final: 0.7807 (mp0) REVERT: B 279 TYR cc_start: 0.8411 (t80) cc_final: 0.8206 (t80) REVERT: B 362 TYR cc_start: 0.8337 (t80) cc_final: 0.8005 (t80) REVERT: C 41 GLN cc_start: 0.8270 (tt0) cc_final: 0.8035 (tm-30) REVERT: C 43 VAL cc_start: 0.8524 (t) cc_final: 0.7521 (t) REVERT: C 80 ASP cc_start: 0.7946 (p0) cc_final: 0.7112 (p0) REVERT: C 81 ASP cc_start: 0.8327 (m-30) cc_final: 0.7944 (m-30) REVERT: C 113 LYS cc_start: 0.9056 (ptmt) cc_final: 0.8726 (ttpt) REVERT: C 161 HIS cc_start: 0.9172 (p90) cc_final: 0.8926 (p-80) REVERT: C 269 MET cc_start: 0.7634 (tpp) cc_final: 0.7420 (tpp) REVERT: C 283 MET cc_start: 0.8606 (mmm) cc_final: 0.8401 (mmm) REVERT: C 292 ASP cc_start: 0.8224 (m-30) cc_final: 0.7777 (t0) REVERT: C 305 MET cc_start: 0.8702 (mmm) cc_final: 0.8397 (mmt) REVERT: C 340 TRP cc_start: 0.9211 (t60) cc_final: 0.8698 (t60) REVERT: D 43 VAL cc_start: 0.8443 (t) cc_final: 0.8237 (t) REVERT: D 47 MET cc_start: 0.5966 (mtm) cc_final: 0.4923 (ttt) REVERT: D 49 GLN cc_start: 0.7739 (pm20) cc_final: 0.7409 (pm20) REVERT: D 105 LEU cc_start: 0.9143 (mp) cc_final: 0.8837 (mp) REVERT: D 154 ASP cc_start: 0.8414 (t0) cc_final: 0.8202 (t0) REVERT: D 162 ASN cc_start: 0.8427 (t0) cc_final: 0.8186 (p0) REVERT: D 217 CYS cc_start: 0.8285 (m) cc_final: 0.8001 (m) REVERT: D 305 MET cc_start: 0.8587 (mmm) cc_final: 0.8308 (tpp) REVERT: D 316 GLU cc_start: 0.8282 (tp30) cc_final: 0.7969 (tp30) REVERT: D 318 THR cc_start: 0.9035 (m) cc_final: 0.8633 (p) REVERT: D 334 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7412 (tp30) REVERT: D 356 TRP cc_start: 0.8663 (m100) cc_final: 0.8246 (m100) REVERT: E 47 MET cc_start: 0.6774 (mtm) cc_final: 0.6383 (ttt) REVERT: E 51 ASP cc_start: 0.7900 (p0) cc_final: 0.7627 (p0) REVERT: E 121 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8405 (mm-40) REVERT: E 283 MET cc_start: 0.8839 (mmp) cc_final: 0.8454 (tpp) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.2374 time to fit residues: 190.8709 Evaluate side-chains 317 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 0.0980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN E 87 HIS E 137 GLN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14960 Z= 0.226 Angle : 0.672 6.345 20305 Z= 0.343 Chirality : 0.046 0.171 2255 Planarity : 0.005 0.047 2595 Dihedral : 6.588 69.805 2085 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.32 % Favored : 95.14 % Rotamer: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1830 helix: 0.71 (0.18), residues: 815 sheet: -0.67 (0.28), residues: 325 loop : -0.71 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 86 HIS 0.008 0.002 HIS C 275 PHE 0.016 0.001 PHE E 255 TYR 0.030 0.001 TYR A 279 ARG 0.006 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 409 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7546 (m-30) cc_final: 0.6891 (t0) REVERT: A 34 ILE cc_start: 0.9628 (mt) cc_final: 0.9380 (tp) REVERT: A 121 GLN cc_start: 0.9036 (pp30) cc_final: 0.8737 (pp30) REVERT: A 154 ASP cc_start: 0.8166 (t70) cc_final: 0.7563 (t70) REVERT: A 176 MET cc_start: 0.8500 (mpp) cc_final: 0.8292 (mpp) REVERT: A 240 TYR cc_start: 0.8761 (t80) cc_final: 0.8446 (t80) REVERT: A 292 ASP cc_start: 0.8014 (m-30) cc_final: 0.7432 (t0) REVERT: B 83 GLU cc_start: 0.9116 (pp20) cc_final: 0.8865 (pp20) REVERT: B 117 GLU cc_start: 0.8553 (pt0) cc_final: 0.8292 (pp20) REVERT: B 166 TYR cc_start: 0.8473 (t80) cc_final: 0.8167 (t80) REVERT: B 192 ILE cc_start: 0.8873 (pt) cc_final: 0.8610 (pt) REVERT: B 269 MET cc_start: 0.8152 (tpp) cc_final: 0.7921 (tpp) REVERT: B 279 TYR cc_start: 0.8456 (t80) cc_final: 0.8109 (t80) REVERT: C 80 ASP cc_start: 0.7786 (p0) cc_final: 0.7003 (p0) REVERT: C 81 ASP cc_start: 0.8449 (m-30) cc_final: 0.8023 (m-30) REVERT: C 82 MET cc_start: 0.8439 (tmm) cc_final: 0.7885 (tmm) REVERT: C 113 LYS cc_start: 0.9150 (ptmt) cc_final: 0.8866 (ttpt) REVERT: C 119 MET cc_start: 0.9428 (ttp) cc_final: 0.9220 (ttp) REVERT: C 161 HIS cc_start: 0.9265 (p90) cc_final: 0.8924 (p90) REVERT: C 269 MET cc_start: 0.7735 (tpp) cc_final: 0.7331 (tpp) REVERT: C 276 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7862 (tm-30) REVERT: C 288 ASP cc_start: 0.7080 (t70) cc_final: 0.6862 (t0) REVERT: C 292 ASP cc_start: 0.8084 (m-30) cc_final: 0.7854 (t0) REVERT: C 305 MET cc_start: 0.8652 (mmm) cc_final: 0.8328 (mmt) REVERT: C 340 TRP cc_start: 0.9207 (t60) cc_final: 0.8684 (t60) REVERT: D 43 VAL cc_start: 0.8291 (t) cc_final: 0.7805 (t) REVERT: D 47 MET cc_start: 0.5977 (mtm) cc_final: 0.4717 (ttt) REVERT: D 49 GLN cc_start: 0.7997 (pm20) cc_final: 0.7606 (pm20) REVERT: D 72 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8125 (tm-30) REVERT: D 75 ILE cc_start: 0.9414 (mt) cc_final: 0.9036 (pt) REVERT: D 147 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7834 (mmm-85) REVERT: D 184 ASP cc_start: 0.8362 (t70) cc_final: 0.8126 (t70) REVERT: D 299 MET cc_start: 0.8281 (mtt) cc_final: 0.8031 (mtt) REVERT: D 305 MET cc_start: 0.8510 (mmm) cc_final: 0.7939 (tpp) REVERT: D 318 THR cc_start: 0.8983 (m) cc_final: 0.8689 (p) REVERT: D 369 ILE cc_start: 0.9008 (tp) cc_final: 0.8778 (tp) REVERT: E 43 VAL cc_start: 0.8473 (t) cc_final: 0.8067 (t) REVERT: E 47 MET cc_start: 0.6755 (mtm) cc_final: 0.6205 (ttt) REVERT: E 72 GLU cc_start: 0.8910 (pp20) cc_final: 0.8494 (pp20) REVERT: E 80 ASP cc_start: 0.8632 (t70) cc_final: 0.8319 (t0) REVERT: E 137 GLN cc_start: 0.8841 (mt0) cc_final: 0.8061 (mm-40) REVERT: E 283 MET cc_start: 0.8874 (mmp) cc_final: 0.8487 (tpp) outliers start: 1 outliers final: 0 residues processed: 410 average time/residue: 0.2249 time to fit residues: 140.2205 Evaluate side-chains 285 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS E 12 ASN E 40 HIS ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14960 Z= 0.253 Angle : 0.677 7.958 20305 Z= 0.342 Chirality : 0.046 0.165 2255 Planarity : 0.004 0.037 2595 Dihedral : 6.408 62.131 2085 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.08 % Favored : 94.54 % Rotamer: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1830 helix: 0.70 (0.18), residues: 820 sheet: -0.72 (0.29), residues: 330 loop : -0.38 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 356 HIS 0.006 0.001 HIS E 161 PHE 0.013 0.001 PHE A 255 TYR 0.030 0.002 TYR A 279 ARG 0.004 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7533 (m-30) cc_final: 0.7145 (t0) REVERT: A 34 ILE cc_start: 0.9614 (mt) cc_final: 0.9405 (tp) REVERT: A 121 GLN cc_start: 0.9094 (pp30) cc_final: 0.8887 (pp30) REVERT: A 154 ASP cc_start: 0.8440 (t70) cc_final: 0.7901 (t70) REVERT: A 217 CYS cc_start: 0.8517 (m) cc_final: 0.8298 (m) REVERT: A 292 ASP cc_start: 0.8100 (m-30) cc_final: 0.7549 (t0) REVERT: A 313 MET cc_start: 0.8691 (tpp) cc_final: 0.8437 (ttm) REVERT: B 83 GLU cc_start: 0.9030 (pp20) cc_final: 0.8758 (pt0) REVERT: B 91 TYR cc_start: 0.9045 (m-80) cc_final: 0.8620 (m-10) REVERT: B 113 LYS cc_start: 0.9088 (ptmt) cc_final: 0.8770 (pttt) REVERT: B 269 MET cc_start: 0.8224 (tpp) cc_final: 0.7957 (tpp) REVERT: B 279 TYR cc_start: 0.8599 (t80) cc_final: 0.8305 (t80) REVERT: C 80 ASP cc_start: 0.7853 (p0) cc_final: 0.7467 (p0) REVERT: C 82 MET cc_start: 0.8396 (tmm) cc_final: 0.7961 (tmm) REVERT: C 113 LYS cc_start: 0.9215 (ptmt) cc_final: 0.8959 (ttpt) REVERT: C 161 HIS cc_start: 0.9290 (p90) cc_final: 0.8432 (p90) REVERT: C 222 ASP cc_start: 0.7123 (p0) cc_final: 0.6824 (p0) REVERT: C 269 MET cc_start: 0.7702 (tpp) cc_final: 0.7333 (tpp) REVERT: C 276 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 288 ASP cc_start: 0.7167 (t70) cc_final: 0.6955 (t70) REVERT: C 292 ASP cc_start: 0.8126 (m-30) cc_final: 0.7892 (t0) REVERT: C 305 MET cc_start: 0.8704 (mmm) cc_final: 0.8146 (tpp) REVERT: D 43 VAL cc_start: 0.8408 (t) cc_final: 0.8170 (t) REVERT: D 72 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8226 (tm-30) REVERT: D 75 ILE cc_start: 0.9449 (mt) cc_final: 0.9071 (pt) REVERT: D 82 MET cc_start: 0.9063 (tmm) cc_final: 0.8718 (tmm) REVERT: D 113 LYS cc_start: 0.8935 (ptmt) cc_final: 0.8630 (ptpt) REVERT: D 283 MET cc_start: 0.8436 (mmp) cc_final: 0.7954 (mmp) REVERT: D 288 ASP cc_start: 0.7807 (t70) cc_final: 0.7431 (t70) REVERT: D 305 MET cc_start: 0.8603 (mmm) cc_final: 0.8132 (tpp) REVERT: D 318 THR cc_start: 0.9007 (m) cc_final: 0.8763 (p) REVERT: E 43 VAL cc_start: 0.8646 (t) cc_final: 0.8446 (t) REVERT: E 72 GLU cc_start: 0.9073 (pp20) cc_final: 0.8635 (pp20) REVERT: E 80 ASP cc_start: 0.8587 (t70) cc_final: 0.8194 (t0) REVERT: E 137 GLN cc_start: 0.9014 (mt0) cc_final: 0.8148 (mm-40) REVERT: E 283 MET cc_start: 0.8843 (mmp) cc_final: 0.8514 (tpp) REVERT: E 305 MET cc_start: 0.7738 (mmt) cc_final: 0.7226 (mmt) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.2364 time to fit residues: 135.0406 Evaluate side-chains 258 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS E 111 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14960 Z= 0.300 Angle : 0.699 6.632 20305 Z= 0.356 Chirality : 0.046 0.175 2255 Planarity : 0.005 0.042 2595 Dihedral : 6.477 64.758 2085 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.25 % Favored : 94.54 % Rotamer: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1830 helix: 0.72 (0.18), residues: 825 sheet: -0.67 (0.29), residues: 325 loop : -0.54 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 86 HIS 0.012 0.002 HIS E 371 PHE 0.017 0.001 PHE A 255 TYR 0.021 0.002 TYR A 279 ARG 0.006 0.001 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 349 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7980 (m-30) cc_final: 0.7480 (t0) REVERT: A 41 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7926 (tm-30) REVERT: A 47 MET cc_start: 0.4901 (ptm) cc_final: 0.4620 (ptt) REVERT: A 121 GLN cc_start: 0.9277 (pp30) cc_final: 0.8916 (pp30) REVERT: A 154 ASP cc_start: 0.8506 (t70) cc_final: 0.7996 (t70) REVERT: A 166 TYR cc_start: 0.8223 (t80) cc_final: 0.7993 (t80) REVERT: A 292 ASP cc_start: 0.8103 (m-30) cc_final: 0.7490 (t0) REVERT: B 91 TYR cc_start: 0.9066 (m-80) cc_final: 0.8616 (m-10) REVERT: B 113 LYS cc_start: 0.8998 (ptmt) cc_final: 0.8730 (pttt) REVERT: B 283 MET cc_start: 0.8522 (mmt) cc_final: 0.8187 (mmm) REVERT: C 82 MET cc_start: 0.8439 (tmm) cc_final: 0.7963 (tmm) REVERT: C 190 MET cc_start: 0.8669 (mtm) cc_final: 0.8368 (mtt) REVERT: C 276 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7951 (tm-30) REVERT: C 288 ASP cc_start: 0.7289 (t70) cc_final: 0.7006 (t70) REVERT: C 292 ASP cc_start: 0.8158 (m-30) cc_final: 0.7629 (t0) REVERT: C 305 MET cc_start: 0.8812 (mmm) cc_final: 0.8510 (mmt) REVERT: D 72 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8284 (tm-30) REVERT: D 75 ILE cc_start: 0.9502 (mt) cc_final: 0.9096 (pt) REVERT: D 82 MET cc_start: 0.8996 (tmm) cc_final: 0.8791 (tmm) REVERT: D 217 CYS cc_start: 0.8305 (m) cc_final: 0.7813 (m) REVERT: D 305 MET cc_start: 0.8585 (mmm) cc_final: 0.8229 (tpp) REVERT: D 318 THR cc_start: 0.9025 (m) cc_final: 0.8794 (p) REVERT: D 356 TRP cc_start: 0.8865 (m100) cc_final: 0.8655 (m100) REVERT: E 72 GLU cc_start: 0.9174 (pp20) cc_final: 0.8742 (pp20) REVERT: E 80 ASP cc_start: 0.8728 (t70) cc_final: 0.8332 (t0) REVERT: E 137 GLN cc_start: 0.9047 (mt0) cc_final: 0.8074 (mm-40) REVERT: E 140 LEU cc_start: 0.9192 (mt) cc_final: 0.8742 (mp) REVERT: E 157 ASP cc_start: 0.7588 (t0) cc_final: 0.7338 (t70) REVERT: E 283 MET cc_start: 0.8806 (mmp) cc_final: 0.8527 (tpp) outliers start: 1 outliers final: 0 residues processed: 350 average time/residue: 0.2243 time to fit residues: 122.1429 Evaluate side-chains 256 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14960 Z= 0.356 Angle : 0.735 7.877 20305 Z= 0.373 Chirality : 0.047 0.191 2255 Planarity : 0.005 0.039 2595 Dihedral : 6.701 64.968 2085 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.41 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1830 helix: 0.64 (0.18), residues: 820 sheet: -0.74 (0.29), residues: 325 loop : -0.49 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 86 HIS 0.013 0.002 HIS A 101 PHE 0.018 0.001 PHE B 255 TYR 0.023 0.002 TYR B 198 ARG 0.005 0.001 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5057 (ptm) cc_final: 0.4685 (ptt) REVERT: A 121 GLN cc_start: 0.9259 (pp30) cc_final: 0.8980 (pp30) REVERT: A 154 ASP cc_start: 0.8478 (t70) cc_final: 0.7951 (t70) REVERT: A 166 TYR cc_start: 0.8305 (t80) cc_final: 0.8069 (t80) REVERT: A 217 CYS cc_start: 0.8550 (m) cc_final: 0.8345 (m) REVERT: A 292 ASP cc_start: 0.8084 (m-30) cc_final: 0.7846 (t0) REVERT: B 91 TYR cc_start: 0.9080 (m-80) cc_final: 0.8589 (m-10) REVERT: B 199 SER cc_start: 0.8210 (m) cc_final: 0.7709 (p) REVERT: B 305 MET cc_start: 0.9250 (mmm) cc_final: 0.8311 (mmt) REVERT: C 190 MET cc_start: 0.8592 (mtm) cc_final: 0.8302 (mtt) REVERT: C 276 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8017 (tm-30) REVERT: C 288 ASP cc_start: 0.7205 (t70) cc_final: 0.6942 (t70) REVERT: C 292 ASP cc_start: 0.8033 (m-30) cc_final: 0.7616 (t0) REVERT: C 305 MET cc_start: 0.8847 (mmm) cc_final: 0.8535 (mmt) REVERT: D 47 MET cc_start: 0.0162 (ttt) cc_final: -0.0156 (ttt) REVERT: D 75 ILE cc_start: 0.9509 (mt) cc_final: 0.9148 (pt) REVERT: D 82 MET cc_start: 0.8974 (tmm) cc_final: 0.8756 (tmm) REVERT: D 113 LYS cc_start: 0.8863 (ptmt) cc_final: 0.8642 (ptpt) REVERT: D 217 CYS cc_start: 0.8113 (m) cc_final: 0.7823 (m) REVERT: D 305 MET cc_start: 0.8646 (mmm) cc_final: 0.8332 (tpp) REVERT: D 318 THR cc_start: 0.9019 (m) cc_final: 0.8794 (p) REVERT: D 356 TRP cc_start: 0.8813 (m100) cc_final: 0.8534 (m100) REVERT: E 72 GLU cc_start: 0.9232 (pp20) cc_final: 0.8821 (pp20) REVERT: E 80 ASP cc_start: 0.8741 (t70) cc_final: 0.8379 (t0) REVERT: E 100 GLU cc_start: 0.7970 (tt0) cc_final: 0.7650 (tt0) REVERT: E 101 HIS cc_start: 0.8124 (p-80) cc_final: 0.7265 (p-80) REVERT: E 140 LEU cc_start: 0.9221 (mt) cc_final: 0.8709 (mp) REVERT: E 154 ASP cc_start: 0.8653 (t0) cc_final: 0.8428 (t0) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2183 time to fit residues: 110.9324 Evaluate side-chains 247 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 137 GLN A 225 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN C 41 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14960 Z= 0.190 Angle : 0.659 8.342 20305 Z= 0.332 Chirality : 0.045 0.194 2255 Planarity : 0.004 0.038 2595 Dihedral : 6.495 65.713 2085 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.75 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 0.02 (0.20), residues: 1830 helix: 0.76 (0.18), residues: 820 sheet: -0.60 (0.29), residues: 325 loop : -0.43 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 86 HIS 0.009 0.001 HIS A 101 PHE 0.011 0.001 PHE E 255 TYR 0.018 0.001 TYR B 362 ARG 0.005 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.4990 (ptm) cc_final: 0.4730 (ptt) REVERT: A 121 GLN cc_start: 0.9389 (pp30) cc_final: 0.9150 (pp30) REVERT: A 154 ASP cc_start: 0.8203 (t70) cc_final: 0.7645 (t70) REVERT: A 217 CYS cc_start: 0.8377 (m) cc_final: 0.8121 (m) REVERT: A 246 GLN cc_start: 0.8702 (mp10) cc_final: 0.8495 (mp10) REVERT: A 305 MET cc_start: 0.8756 (mmm) cc_final: 0.8033 (tpp) REVERT: B 91 TYR cc_start: 0.9062 (m-80) cc_final: 0.8679 (m-10) REVERT: B 199 SER cc_start: 0.7804 (m) cc_final: 0.7463 (p) REVERT: B 283 MET cc_start: 0.8722 (mmt) cc_final: 0.8051 (mpp) REVERT: B 305 MET cc_start: 0.9185 (mmm) cc_final: 0.8338 (mmt) REVERT: C 118 LYS cc_start: 0.9256 (tptt) cc_final: 0.8837 (tptm) REVERT: C 253 GLU cc_start: 0.8136 (mp0) cc_final: 0.7814 (mp0) REVERT: C 276 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7863 (tm-30) REVERT: C 288 ASP cc_start: 0.7153 (t70) cc_final: 0.6867 (t70) REVERT: C 292 ASP cc_start: 0.8100 (m-30) cc_final: 0.7653 (t0) REVERT: C 299 MET cc_start: 0.8790 (ttm) cc_final: 0.8350 (mtp) REVERT: D 47 MET cc_start: 0.0287 (ttt) cc_final: -0.0063 (ttt) REVERT: D 137 GLN cc_start: 0.8457 (mt0) cc_final: 0.8212 (mm-40) REVERT: D 147 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7443 (mtp85) REVERT: D 180 LEU cc_start: 0.8991 (tp) cc_final: 0.8783 (tp) REVERT: D 283 MET cc_start: 0.8453 (mmp) cc_final: 0.8017 (mmp) REVERT: D 305 MET cc_start: 0.8566 (mmm) cc_final: 0.8297 (tpp) REVERT: D 318 THR cc_start: 0.9007 (m) cc_final: 0.8778 (p) REVERT: E 72 GLU cc_start: 0.9245 (pp20) cc_final: 0.8825 (pp20) REVERT: E 80 ASP cc_start: 0.8646 (t70) cc_final: 0.8239 (t0) REVERT: E 100 GLU cc_start: 0.8028 (tt0) cc_final: 0.7744 (tt0) REVERT: E 101 HIS cc_start: 0.7989 (p-80) cc_final: 0.7250 (p-80) REVERT: E 154 ASP cc_start: 0.8570 (t0) cc_final: 0.8329 (t0) REVERT: E 280 ASN cc_start: 0.8629 (m110) cc_final: 0.8375 (m-40) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2104 time to fit residues: 115.7944 Evaluate side-chains 261 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14960 Z= 0.367 Angle : 0.747 10.097 20305 Z= 0.379 Chirality : 0.047 0.203 2255 Planarity : 0.005 0.039 2595 Dihedral : 6.725 62.720 2085 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.36 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1830 helix: 0.64 (0.18), residues: 825 sheet: -0.66 (0.29), residues: 320 loop : -0.59 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 356 HIS 0.011 0.002 HIS B 101 PHE 0.016 0.001 PHE B 255 TYR 0.024 0.002 TYR A 166 ARG 0.005 0.001 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLN cc_start: 0.9451 (pp30) cc_final: 0.9082 (pp30) REVERT: A 154 ASP cc_start: 0.8457 (t70) cc_final: 0.8047 (t70) REVERT: A 305 MET cc_start: 0.8872 (mmm) cc_final: 0.8136 (tpp) REVERT: B 91 TYR cc_start: 0.9084 (m-80) cc_final: 0.8639 (m-10) REVERT: B 192 ILE cc_start: 0.8617 (mm) cc_final: 0.7887 (tp) REVERT: B 199 SER cc_start: 0.8032 (m) cc_final: 0.7708 (p) REVERT: B 280 ASN cc_start: 0.8559 (m110) cc_final: 0.8294 (m-40) REVERT: B 305 MET cc_start: 0.9244 (mmm) cc_final: 0.8332 (mmt) REVERT: C 118 LYS cc_start: 0.9311 (tptt) cc_final: 0.8931 (tptm) REVERT: C 276 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8058 (tm-30) REVERT: C 288 ASP cc_start: 0.7158 (t70) cc_final: 0.6872 (t70) REVERT: C 292 ASP cc_start: 0.8079 (m-30) cc_final: 0.7630 (t0) REVERT: C 299 MET cc_start: 0.8857 (ttm) cc_final: 0.8398 (mtp) REVERT: C 305 MET cc_start: 0.8695 (mmm) cc_final: 0.8327 (tpp) REVERT: D 47 MET cc_start: 0.0025 (ttt) cc_final: -0.0348 (ttt) REVERT: D 72 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8399 (tm-30) REVERT: D 75 ILE cc_start: 0.9522 (mt) cc_final: 0.9144 (pt) REVERT: D 147 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7702 (mtp85) REVERT: D 305 MET cc_start: 0.8654 (mmm) cc_final: 0.8356 (tpp) REVERT: D 318 THR cc_start: 0.9054 (m) cc_final: 0.8842 (p) REVERT: D 356 TRP cc_start: 0.8742 (m100) cc_final: 0.8491 (m-10) REVERT: E 72 GLU cc_start: 0.9259 (pp20) cc_final: 0.8885 (pp20) REVERT: E 80 ASP cc_start: 0.8753 (t70) cc_final: 0.8349 (t0) REVERT: E 154 ASP cc_start: 0.8650 (t0) cc_final: 0.8324 (t0) REVERT: E 305 MET cc_start: 0.8007 (mmt) cc_final: 0.7378 (tpt) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2090 time to fit residues: 105.5827 Evaluate side-chains 239 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 chunk 100 optimal weight: 0.0970 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.6917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14960 Z= 0.185 Angle : 0.687 9.172 20305 Z= 0.341 Chirality : 0.045 0.201 2255 Planarity : 0.004 0.044 2595 Dihedral : 6.481 64.231 2085 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.08 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1830 helix: 0.69 (0.18), residues: 820 sheet: -0.34 (0.31), residues: 295 loop : -0.46 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 86 HIS 0.006 0.001 HIS E 161 PHE 0.013 0.001 PHE B 124 TYR 0.024 0.001 TYR A 166 ARG 0.005 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.4429 (ptt) cc_final: 0.4064 (ptt) REVERT: A 82 MET cc_start: 0.8534 (tmm) cc_final: 0.8230 (tmm) REVERT: A 107 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 111 ASN cc_start: 0.8742 (p0) cc_final: 0.8435 (p0) REVERT: A 154 ASP cc_start: 0.8254 (t70) cc_final: 0.7777 (t70) REVERT: A 246 GLN cc_start: 0.8836 (mp10) cc_final: 0.8568 (mp10) REVERT: A 283 MET cc_start: 0.8740 (mmm) cc_final: 0.8526 (mmp) REVERT: A 305 MET cc_start: 0.8729 (mmm) cc_final: 0.7897 (tpp) REVERT: A 340 TRP cc_start: 0.9095 (t60) cc_final: 0.8411 (t60) REVERT: B 91 TYR cc_start: 0.8980 (m-80) cc_final: 0.8595 (m-10) REVERT: B 280 ASN cc_start: 0.8269 (m110) cc_final: 0.7830 (m110) REVERT: B 305 MET cc_start: 0.9165 (mmm) cc_final: 0.8596 (tpp) REVERT: C 44 MET cc_start: 0.7706 (tpp) cc_final: 0.7231 (tpt) REVERT: C 118 LYS cc_start: 0.9233 (tptt) cc_final: 0.8839 (tptm) REVERT: C 276 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7894 (tm-30) REVERT: C 292 ASP cc_start: 0.8148 (m-30) cc_final: 0.7633 (t0) REVERT: C 299 MET cc_start: 0.8769 (ttm) cc_final: 0.8339 (mtp) REVERT: C 305 MET cc_start: 0.8726 (mmm) cc_final: 0.8393 (tpp) REVERT: D 47 MET cc_start: -0.0406 (ttt) cc_final: -0.0714 (ttt) REVERT: D 147 ARG cc_start: 0.8021 (mmm-85) cc_final: 0.7531 (mtp85) REVERT: D 176 MET cc_start: 0.8628 (mmm) cc_final: 0.8340 (tpp) REVERT: D 305 MET cc_start: 0.8603 (mmm) cc_final: 0.8346 (tpp) REVERT: D 318 THR cc_start: 0.8991 (m) cc_final: 0.8772 (p) REVERT: E 72 GLU cc_start: 0.9221 (pp20) cc_final: 0.8860 (pp20) REVERT: E 80 ASP cc_start: 0.8617 (t70) cc_final: 0.8239 (t0) REVERT: E 154 ASP cc_start: 0.8460 (t0) cc_final: 0.8092 (t0) REVERT: E 305 MET cc_start: 0.7877 (mmt) cc_final: 0.7131 (tpt) REVERT: E 325 MET cc_start: 0.7887 (mmm) cc_final: 0.7208 (mmm) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.2107 time to fit residues: 117.6621 Evaluate side-chains 263 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 0.0030 chunk 122 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 169 optimal weight: 0.3980 chunk 146 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS C 12 ASN C 87 HIS C 297 ASN D 173 HIS ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 40 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 14960 Z= 0.199 Angle : 0.685 10.622 20305 Z= 0.341 Chirality : 0.045 0.203 2255 Planarity : 0.004 0.041 2595 Dihedral : 6.273 62.243 2085 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.68 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1830 helix: 0.79 (0.18), residues: 790 sheet: -0.41 (0.31), residues: 300 loop : -0.43 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 86 HIS 0.008 0.001 HIS D 371 PHE 0.012 0.001 PHE D 352 TYR 0.025 0.001 TYR A 166 ARG 0.005 0.000 ARG A 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8035 (t0) cc_final: 0.7832 (t0) REVERT: A 111 ASN cc_start: 0.8746 (p0) cc_final: 0.8515 (p0) REVERT: A 154 ASP cc_start: 0.8105 (t70) cc_final: 0.7590 (t70) REVERT: A 283 MET cc_start: 0.8815 (mmm) cc_final: 0.8368 (mmp) REVERT: A 305 MET cc_start: 0.8741 (mmm) cc_final: 0.8015 (ttp) REVERT: A 340 TRP cc_start: 0.9071 (t60) cc_final: 0.8416 (t60) REVERT: B 43 VAL cc_start: 0.8514 (t) cc_final: 0.8242 (t) REVERT: B 91 TYR cc_start: 0.8991 (m-80) cc_final: 0.8603 (m-10) REVERT: B 276 GLU cc_start: 0.8620 (tp30) cc_final: 0.8210 (tm-30) REVERT: B 280 ASN cc_start: 0.8490 (m110) cc_final: 0.7226 (m110) REVERT: B 305 MET cc_start: 0.9173 (mmm) cc_final: 0.8587 (tpp) REVERT: C 81 ASP cc_start: 0.8289 (m-30) cc_final: 0.7997 (m-30) REVERT: C 118 LYS cc_start: 0.9251 (tptt) cc_final: 0.9018 (mmtp) REVERT: C 121 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8132 (tm-30) REVERT: C 253 GLU cc_start: 0.7649 (mp0) cc_final: 0.7392 (mp0) REVERT: C 292 ASP cc_start: 0.8068 (m-30) cc_final: 0.7599 (t0) REVERT: C 299 MET cc_start: 0.8748 (ttm) cc_final: 0.8304 (mtp) REVERT: C 305 MET cc_start: 0.8697 (mmm) cc_final: 0.8425 (tpp) REVERT: D 176 MET cc_start: 0.8552 (mmm) cc_final: 0.8307 (tpp) REVERT: D 180 LEU cc_start: 0.8959 (tp) cc_final: 0.8752 (tp) REVERT: D 184 ASP cc_start: 0.8231 (t70) cc_final: 0.8013 (t0) REVERT: D 305 MET cc_start: 0.8593 (mmm) cc_final: 0.8331 (tpp) REVERT: D 318 THR cc_start: 0.8995 (m) cc_final: 0.8787 (p) REVERT: E 72 GLU cc_start: 0.9240 (pp20) cc_final: 0.8860 (pp20) REVERT: E 80 ASP cc_start: 0.8701 (t70) cc_final: 0.8154 (t0) REVERT: E 154 ASP cc_start: 0.8498 (t0) cc_final: 0.8118 (t0) REVERT: E 305 MET cc_start: 0.7807 (mmt) cc_final: 0.7330 (tpp) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2181 time to fit residues: 120.0952 Evaluate side-chains 255 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 371 HIS D 353 GLN E 40 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.082821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.071894 restraints weight = 37225.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.074580 restraints weight = 19518.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.076406 restraints weight = 11762.876| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14960 Z= 0.303 Angle : 0.724 9.420 20305 Z= 0.366 Chirality : 0.047 0.192 2255 Planarity : 0.005 0.043 2595 Dihedral : 6.403 61.066 2085 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.63 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1830 helix: 0.78 (0.19), residues: 780 sheet: -0.43 (0.31), residues: 300 loop : -0.50 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP E 86 HIS 0.006 0.001 HIS B 161 PHE 0.012 0.001 PHE B 255 TYR 0.023 0.002 TYR A 166 ARG 0.009 0.001 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3170.11 seconds wall clock time: 57 minutes 26.85 seconds (3446.85 seconds total)