Starting phenix.real_space_refine on Mon Mar 11 17:27:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/03_2024/8w8b_37351_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/03_2024/8w8b_37351.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/03_2024/8w8b_37351_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/03_2024/8w8b_37351_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/03_2024/8w8b_37351_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/03_2024/8w8b_37351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/03_2024/8w8b_37351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/03_2024/8w8b_37351_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/03_2024/8w8b_37351_updated.pdb" } resolution = 3.0 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= -0.002 sd= 0.152 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5613 2.51 5 N 1459 2.21 5 O 1598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "R TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8734 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1751 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2513 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1756 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 1 Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2197 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 2 Chain: "R" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 170 Unusual residues: {'CLR': 5, 'PLM': 1, 'UJL': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 5.55, per 1000 atoms: 0.64 Number of scatterers: 8734 At special positions: 0 Unit cell: (86.52, 115.36, 128.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1598 8.00 N 1459 7.00 C 5613 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 - 3.50 Amino acid : False - 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: 3.12 Conformation dependent library (CDL) restraints added in 1.6 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 12 sheets defined 36.7% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.585A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.021A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.692A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.457A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'G' and resid 19 through 24 removed outlier: 4.465A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 36 through 63 Processing helix chain 'R' and resid 65 through 67 No H-bonds generated for 'chain 'R' and resid 65 through 67' Processing helix chain 'R' and resid 70 through 99 removed outlier: 4.402A pdb=" N LEU R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 105 through 139 Processing helix chain 'R' and resid 141 through 146 Processing helix chain 'R' and resid 150 through 173 Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 193 through 203 Processing helix chain 'R' and resid 205 through 227 Processing helix chain 'R' and resid 326 through 371 Proline residue: R 360 - end of helix Proline residue: R 369 - end of helix Processing helix chain 'R' and resid 379 through 400 removed outlier: 3.800A pdb=" N ASN R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 405 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.676A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.960A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.782A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.662A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.604A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.659A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.381A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.600A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 4 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.030A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 7.000A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1179 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: 2.91 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2760 1.34 - 1.46: 1943 1.46 - 1.58: 4132 1.58 - 1.69: 1 1.69 - 1.81: 90 Bond restraints: 8926 Sorted by residual: bond pdb=" C3 UJL R 507 " pdb=" O1 UJL R 507 " ideal model delta sigma weight residual 1.460 1.421 0.039 2.00e-02 2.50e+03 3.84e+00 bond pdb=" C6 UJL R 507 " pdb=" C9 UJL R 507 " ideal model delta sigma weight residual 1.428 1.390 0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" N TYR R 35 " pdb=" CA TYR R 35 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N GLN G 18 " pdb=" CA GLN G 18 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 ... (remaining 8921 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.26: 196 106.26 - 113.20: 4949 113.20 - 120.13: 3075 120.13 - 127.07: 3790 127.07 - 134.00: 100 Bond angle restraints: 12110 Sorted by residual: angle pdb=" N ARG A 242 " pdb=" CA ARG A 242 " pdb=" C ARG A 242 " ideal model delta sigma weight residual 112.89 108.28 4.61 1.24e+00 6.50e-01 1.38e+01 angle pdb=" N THR B 128 " pdb=" CA THR B 128 " pdb=" CB THR B 128 " ideal model delta sigma weight residual 109.97 115.34 -5.37 1.47e+00 4.63e-01 1.33e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 113.21 109.45 3.76 1.15e+00 7.56e-01 1.07e+01 angle pdb=" N SER B 245 " pdb=" CA SER B 245 " pdb=" C SER B 245 " ideal model delta sigma weight residual 109.69 114.17 -4.48 1.44e+00 4.82e-01 9.69e+00 angle pdb=" N SER B 245 " pdb=" CA SER B 245 " pdb=" CB SER B 245 " ideal model delta sigma weight residual 110.87 107.18 3.69 1.51e+00 4.39e-01 5.96e+00 ... (remaining 12105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4986 17.94 - 35.87: 408 35.87 - 53.80: 105 53.80 - 71.74: 23 71.74 - 89.67: 7 Dihedral angle restraints: 5529 sinusoidal: 2356 harmonic: 3173 Sorted by residual: dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA LEU B 117 " pdb=" C LEU B 117 " pdb=" N ASP B 118 " pdb=" CA ASP B 118 " ideal model delta harmonic sigma weight residual 180.00 162.30 17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CG ARG G 62 " pdb=" CD ARG G 62 " pdb=" NE ARG G 62 " pdb=" CZ ARG G 62 " ideal model delta sinusoidal sigma weight residual 90.00 41.43 48.57 2 1.50e+01 4.44e-03 1.20e+01 ... (remaining 5526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1070 0.040 - 0.080: 221 0.080 - 0.120: 80 0.120 - 0.159: 13 0.159 - 0.199: 2 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA THR B 128 " pdb=" N THR B 128 " pdb=" C THR B 128 " pdb=" CB THR B 128 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" C3 UJL R 507 " pdb=" C2 UJL R 507 " pdb=" C9 UJL R 507 " pdb=" O1 UJL R 507 " both_signs ideal model delta sigma weight residual False -2.48 -2.32 -0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CB VAL R 98 " pdb=" CA VAL R 98 " pdb=" CG1 VAL R 98 " pdb=" CG2 VAL R 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 1383 not shown) Planarity restraints: 1492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 62 " 0.172 9.50e-02 1.11e+02 7.74e-02 4.24e+00 pdb=" NE ARG G 62 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG G 62 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 62 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 62 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO E 236 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 219 " 0.112 9.50e-02 1.11e+02 5.02e-02 1.84e+00 pdb=" NE ARG B 219 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 219 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 219 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 219 " 0.001 2.00e-02 2.50e+03 ... (remaining 1489 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 113 2.63 - 3.20: 7811 3.20 - 3.77: 13243 3.77 - 4.33: 19418 4.33 - 4.90: 32920 Nonbonded interactions: 73505 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.063 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.182 2.440 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.200 2.440 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.207 2.440 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.232 2.440 ... (remaining 73500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.020 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: 4.060 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.160 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.003 0.039 8926 Z= 0.202 Angle : 0.532 5.368 12110 Z= 0.306 Chirality : 0.040 0.199 1386 Planarity : 0.004 0.077 1492 Dihedral : 14.539 89.673 3483 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.54 % Allowed : 14.72 % Favored : 84.75 % 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: 1.35 (0.26), residues: 1076 helix: 2.56 (0.27), residues: 375 sheet: 0.50 (0.31), residues: 275 loop : -0.32 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS A 213 PHE 0.020 0.001 PHE B 292 TYR 0.010 0.001 TYR E 190 ARG 0.013 0.001 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 1.016 Fit side-chains REVERT: A 8 GLU cc_start: 0.8761 (pt0) cc_final: 0.8298 (pt0) REVERT: A 275 GLU cc_start: 0.7322 (tp30) cc_final: 0.7075 (tp30) REVERT: E 18 ARG cc_start: 0.8008 (ttt180) cc_final: 0.7770 (tpt170) outliers start: 5 outliers final: 3 residues processed: 112 average time/residue: 1.3150 time to fit residues: 156.6548 Evaluate side-chains 101 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain R residue 61 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8926 Z= 0.216 Angle : 0.527 8.897 12110 Z= 0.279 Chirality : 0.042 0.139 1386 Planarity : 0.004 0.049 1492 Dihedral : 5.715 57.143 1536 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.04 % Allowed : 13.75 % Favored : 84.21 % 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: 1.52 (0.26), residues: 1076 helix: 2.70 (0.27), residues: 374 sheet: 0.75 (0.31), residues: 268 loop : -0.32 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE R 362 TYR 0.012 0.001 TYR E 190 ARG 0.006 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.983 Fit side-chains REVERT: B 270 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7947 (pp) REVERT: B 333 ASP cc_start: 0.7724 (t0) cc_final: 0.7490 (t0) outliers start: 19 outliers final: 5 residues processed: 116 average time/residue: 1.2944 time to fit residues: 159.6540 Evaluate side-chains 100 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain R residue 108 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8926 Z= 0.203 Angle : 0.501 8.578 12110 Z= 0.265 Chirality : 0.041 0.138 1386 Planarity : 0.003 0.044 1492 Dihedral : 5.446 55.816 1531 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.47 % Allowed : 15.25 % Favored : 82.28 % 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: 1076 helix: 2.73 (0.27), residues: 374 sheet: 0.71 (0.30), residues: 268 loop : -0.30 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.011 0.001 PHE R 362 TYR 0.011 0.001 TYR R 198 ARG 0.006 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.038 Fit side-chains REVERT: A 205 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7389 (mpp80) REVERT: A 208 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7815 (ttp-110) REVERT: B 134 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7584 (ptp90) REVERT: B 217 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7181 (pp-130) REVERT: B 270 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8031 (pp) outliers start: 23 outliers final: 8 residues processed: 117 average time/residue: 1.2154 time to fit residues: 151.9706 Evaluate side-chains 103 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 0.0770 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8926 Z= 0.196 Angle : 0.495 8.537 12110 Z= 0.262 Chirality : 0.041 0.138 1386 Planarity : 0.003 0.040 1492 Dihedral : 5.392 52.777 1531 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.33 % Allowed : 15.04 % Favored : 81.63 % 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: 1076 helix: 2.79 (0.27), residues: 373 sheet: 0.68 (0.30), residues: 264 loop : -0.33 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.010 0.001 PHE R 362 TYR 0.011 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 0.994 Fit side-chains REVERT: A 205 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7336 (mpp80) REVERT: B 153 ASP cc_start: 0.8335 (m-30) cc_final: 0.8041 (m-30) REVERT: B 217 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7129 (pp-130) REVERT: B 270 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8147 (pp) REVERT: E 246 GLU cc_start: 0.7009 (pm20) cc_final: 0.6602 (pm20) REVERT: R 68 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7700 (mt0) outliers start: 31 outliers final: 13 residues processed: 121 average time/residue: 1.2633 time to fit residues: 162.8245 Evaluate side-chains 108 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 211 MET Chi-restraints excluded: chain R residue 335 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8926 Z= 0.352 Angle : 0.580 10.906 12110 Z= 0.303 Chirality : 0.044 0.142 1386 Planarity : 0.004 0.046 1492 Dihedral : 6.042 56.574 1531 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.33 % Allowed : 15.79 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1076 helix: 2.47 (0.27), residues: 375 sheet: 0.57 (0.30), residues: 265 loop : -0.44 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.002 PHE A 196 TYR 0.014 0.002 TYR E 190 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 1.015 Fit side-chains REVERT: B 217 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8122 (pp-130) REVERT: B 270 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8167 (pp) REVERT: E 246 GLU cc_start: 0.7128 (pm20) cc_final: 0.6715 (pm20) outliers start: 31 outliers final: 18 residues processed: 115 average time/residue: 1.2009 time to fit residues: 147.9973 Evaluate side-chains 114 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 211 MET Chi-restraints excluded: chain R residue 335 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.0270 chunk 98 optimal weight: 5.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8926 Z= 0.158 Angle : 0.481 8.166 12110 Z= 0.254 Chirality : 0.040 0.134 1386 Planarity : 0.003 0.038 1492 Dihedral : 5.561 52.233 1531 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.36 % Allowed : 17.40 % Favored : 80.24 % 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: 1.48 (0.26), residues: 1076 helix: 2.75 (0.27), residues: 374 sheet: 0.64 (0.30), residues: 255 loop : -0.33 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.010 0.001 PHE R 362 TYR 0.010 0.001 TYR E 190 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.081 Fit side-chains REVERT: B 270 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8242 (pp) REVERT: B 321 THR cc_start: 0.8706 (p) cc_final: 0.8432 (p) REVERT: E 246 GLU cc_start: 0.7043 (pm20) cc_final: 0.6638 (pm20) outliers start: 22 outliers final: 7 residues processed: 110 average time/residue: 1.1253 time to fit residues: 133.0680 Evaluate side-chains 99 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8926 Z= 0.320 Angle : 0.559 10.550 12110 Z= 0.293 Chirality : 0.043 0.139 1386 Planarity : 0.004 0.044 1492 Dihedral : 6.028 58.318 1531 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.90 % Allowed : 17.40 % Favored : 79.70 % 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: 1.24 (0.26), residues: 1076 helix: 2.51 (0.27), residues: 375 sheet: 0.46 (0.30), residues: 267 loop : -0.42 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.002 0.001 HIS B 91 PHE 0.013 0.002 PHE A 196 TYR 0.014 0.002 TYR E 190 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 0.975 Fit side-chains REVERT: B 197 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7961 (ttp-110) REVERT: B 270 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8288 (pp) REVERT: E 246 GLU cc_start: 0.7138 (pm20) cc_final: 0.6740 (pm20) outliers start: 27 outliers final: 13 residues processed: 115 average time/residue: 1.2094 time to fit residues: 148.8567 Evaluate side-chains 106 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 0.0470 chunk 89 optimal weight: 0.5980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 : 0.002 0.036 8926 Z= 0.158 Angle : 0.487 8.104 12110 Z= 0.256 Chirality : 0.040 0.134 1386 Planarity : 0.003 0.038 1492 Dihedral : 5.538 53.485 1531 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.61 % Allowed : 19.12 % Favored : 79.27 % 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: 1.47 (0.26), residues: 1076 helix: 2.73 (0.27), residues: 376 sheet: 0.73 (0.31), residues: 251 loop : -0.39 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 PHE 0.010 0.001 PHE R 362 TYR 0.010 0.001 TYR E 190 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.979 Fit side-chains REVERT: B 134 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7517 (ptt-90) REVERT: B 146 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8422 (tp) REVERT: B 270 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8304 (pp) REVERT: E 38 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8261 (ttp-170) REVERT: E 246 GLU cc_start: 0.7078 (pm20) cc_final: 0.6675 (pm20) outliers start: 15 outliers final: 7 residues processed: 107 average time/residue: 1.2445 time to fit residues: 142.1022 Evaluate side-chains 101 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8926 Z= 0.162 Angle : 0.492 8.165 12110 Z= 0.258 Chirality : 0.040 0.133 1386 Planarity : 0.003 0.037 1492 Dihedral : 5.396 55.801 1531 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.83 % Allowed : 19.66 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 1076 helix: 2.77 (0.27), residues: 376 sheet: 0.54 (0.31), residues: 261 loop : -0.25 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 PHE 0.010 0.001 PHE R 362 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.109 Fit side-chains REVERT: B 134 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7546 (ptt-90) REVERT: B 270 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8306 (pp) REVERT: E 38 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8205 (ttp-170) REVERT: E 246 GLU cc_start: 0.7089 (pm20) cc_final: 0.6806 (pm20) outliers start: 17 outliers final: 9 residues processed: 105 average time/residue: 1.3235 time to fit residues: 148.1774 Evaluate side-chains 104 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 105 optimal weight: 0.0000 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8926 Z= 0.163 Angle : 0.493 8.120 12110 Z= 0.259 Chirality : 0.040 0.132 1386 Planarity : 0.003 0.037 1492 Dihedral : 5.364 57.724 1531 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.40 % Allowed : 19.87 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 1076 helix: 2.74 (0.27), residues: 376 sheet: 0.63 (0.31), residues: 259 loop : -0.29 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 PHE 0.010 0.001 PHE R 362 TYR 0.012 0.001 TYR E 190 ARG 0.007 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.984 Fit side-chains REVERT: B 134 ARG cc_start: 0.7989 (mtm110) cc_final: 0.7608 (ptt-90) REVERT: E 38 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8240 (ttp-170) REVERT: E 246 GLU cc_start: 0.7168 (pm20) cc_final: 0.6889 (pm20) outliers start: 13 outliers final: 9 residues processed: 104 average time/residue: 1.2741 time to fit residues: 141.4633 Evaluate side-chains 104 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.0570 chunk 84 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.148652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112332 restraints weight = 9713.288| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.74 r_work: 0.3019 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8926 Z= 0.151 Angle : 0.486 7.912 12110 Z= 0.255 Chirality : 0.040 0.132 1386 Planarity : 0.003 0.037 1492 Dihedral : 5.291 59.472 1531 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.97 % Allowed : 20.41 % Favored : 78.63 % 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: 1.55 (0.26), residues: 1076 helix: 2.77 (0.27), residues: 377 sheet: 0.63 (0.31), residues: 259 loop : -0.25 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS B 311 PHE 0.009 0.001 PHE R 362 TYR 0.011 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3264.11 seconds wall clock time: 59 minutes 7.12 seconds (3547.12 seconds total)