Starting phenix.real_space_refine on Wed Feb 14 07:24:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ija_35483/02_2024/8ija_35483_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ija_35483/02_2024/8ija_35483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ija_35483/02_2024/8ija_35483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ija_35483/02_2024/8ija_35483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ija_35483/02_2024/8ija_35483_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ija_35483/02_2024/8ija_35483_neut_updated.pdb" } resolution = 2.69 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= 0.024 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 67 5.16 5 C 5653 2.51 5 N 1506 2.21 5 O 1619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S GLU 210": "OE1" <-> "OE2" Residue "S GLU 222": "OE1" <-> "OE2" Residue "S GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8845 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2357 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1699 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2577 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.03, per 1000 atoms: 0.57 Number of scatterers: 8845 At special positions: 0 Unit cell: (87.15, 119.52, 130.31, 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 67 16.00 O 1619 8.00 N 1506 7.00 C 5653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 3.38 Conformation dependent library (CDL) restraints added in 1.8 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 13 sheets defined 32.7% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 24 through 54 removed outlier: 3.572A pdb=" N LEU A 30 " --> pdb=" O ILE A 26 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.610A pdb=" N LEU A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 88 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 129 Processing helix chain 'A' and resid 135 through 138 Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 189 through 217 removed outlier: 3.762A pdb=" N LEU A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 224 through 261 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 272 through 293 removed outlier: 3.689A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'C' and resid 7 through 32 removed outlier: 3.606A pdb=" N ARG C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 271 through 280 removed outlier: 3.507A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 310 removed outlier: 3.862A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 351 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.003A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.782A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 10 through 12 Processing sheet with id= B, first strand: chain 'C' and resid 319 through 323 removed outlier: 6.374A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS C 195 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU C 36 " --> pdb=" O HIS C 195 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS C 197 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU C 38 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE C 199 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLY C 40 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.886A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.034A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.628A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.726A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.720A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.532A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.693A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 4 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.769A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.345A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 143 through 148 389 hydrogen bonds defined for protein. 1116 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: 2.58 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2656 1.34 - 1.46: 2304 1.46 - 1.59: 3981 1.59 - 1.71: 0 1.71 - 1.84: 97 Bond restraints: 9038 Sorted by residual: bond pdb=" ND1 HIS A 9 " pdb=" CE1 HIS A 9 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.83e+01 bond pdb=" ND1 HIS A 259 " pdb=" CE1 HIS A 259 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.78e+01 bond pdb=" CG ASN A 17 " pdb=" OD1 ASN A 17 " ideal model delta sigma weight residual 1.231 1.329 -0.098 1.90e-02 2.77e+03 2.65e+01 bond pdb=" ND1 HIS A 133 " pdb=" CE1 HIS A 133 " ideal model delta sigma weight residual 1.321 1.372 -0.051 1.00e-02 1.00e+04 2.64e+01 bond pdb=" CD2 HIS A 133 " pdb=" NE2 HIS A 133 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.10e-02 8.26e+03 2.37e+01 ... (remaining 9033 not shown) Histogram of bond angle deviations from ideal: 86.44 - 98.39: 10 98.39 - 110.34: 2036 110.34 - 122.29: 8705 122.29 - 134.25: 1487 134.25 - 146.20: 4 Bond angle restraints: 12242 Sorted by residual: angle pdb=" N TYR A 295 " pdb=" CA TYR A 295 " pdb=" C TYR A 295 " ideal model delta sigma weight residual 111.69 146.20 -34.51 1.23e+00 6.61e-01 7.87e+02 angle pdb=" N THR C 324 " pdb=" CA THR C 324 " pdb=" C THR C 324 " ideal model delta sigma weight residual 111.24 142.05 -30.81 1.29e+00 6.01e-01 5.70e+02 angle pdb=" N CYS C 325 " pdb=" CA CYS C 325 " pdb=" C CYS C 325 " ideal model delta sigma weight residual 112.86 134.01 -21.15 1.22e+00 6.72e-01 3.01e+02 angle pdb=" C VAL C 201 " pdb=" CA VAL C 201 " pdb=" CB VAL C 201 " ideal model delta sigma weight residual 111.81 91.92 19.89 1.37e+00 5.33e-01 2.11e+02 angle pdb=" N PHE A 296 " pdb=" CA PHE A 296 " pdb=" CB PHE A 296 " ideal model delta sigma weight residual 110.33 89.57 20.76 1.50e+00 4.44e-01 1.91e+02 ... (remaining 12237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4517 17.82 - 35.64: 590 35.64 - 53.47: 179 53.47 - 71.29: 33 71.29 - 89.11: 18 Dihedral angle restraints: 5337 sinusoidal: 2050 harmonic: 3287 Sorted by residual: dihedral pdb=" C VAL C 201 " pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" CB VAL C 201 " ideal model delta harmonic sigma weight residual -122.00 -90.73 -31.27 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" N PHE A 296 " pdb=" C PHE A 296 " pdb=" CA PHE A 296 " pdb=" CB PHE A 296 " ideal model delta harmonic sigma weight residual 122.80 95.32 27.48 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" C CYS C 325 " pdb=" N CYS C 325 " pdb=" CA CYS C 325 " pdb=" CB CYS C 325 " ideal model delta harmonic sigma weight residual -122.60 -143.50 20.90 0 2.50e+00 1.60e-01 6.99e+01 ... (remaining 5334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 1375 0.260 - 0.519: 5 0.519 - 0.778: 2 0.778 - 1.038: 0 1.038 - 1.297: 4 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA TYR A 295 " pdb=" N TYR A 295 " pdb=" C TYR A 295 " pdb=" CB TYR A 295 " both_signs ideal model delta sigma weight residual False 2.51 1.21 1.30 2.00e-01 2.50e+01 4.21e+01 chirality pdb=" CA ARG A 270 " pdb=" N ARG A 270 " pdb=" C ARG A 270 " pdb=" CB ARG A 270 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.21e+01 chirality pdb=" CA CYS C 325 " pdb=" N CYS C 325 " pdb=" C CYS C 325 " pdb=" CB CYS C 325 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.94e+01 ... (remaining 1383 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " 0.111 2.00e-02 2.50e+03 6.51e-02 8.49e+01 pdb=" CG TYR A 284 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " -0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 91 " -0.099 2.00e-02 2.50e+03 5.25e-02 6.89e+01 pdb=" CG TRP A 91 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP A 91 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 TRP A 91 " 0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP A 91 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP A 91 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 91 " 0.066 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 91 " -0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 91 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP A 91 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 87 " 0.062 2.00e-02 2.50e+03 3.17e-02 2.01e+01 pdb=" CG TYR A 87 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 87 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 87 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 87 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 87 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 87 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 87 " 0.035 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 51 2.41 - 3.04: 5383 3.04 - 3.66: 13447 3.66 - 4.28: 21313 4.28 - 4.90: 35891 Nonbonded interactions: 76085 Sorted by model distance: nonbonded pdb=" O THR C 324 " pdb=" CG2 THR C 327 " model vdw 1.793 3.460 nonbonded pdb=" O ARG A 270 " pdb=" NH1 ARG A 270 " model vdw 1.900 2.520 nonbonded pdb=" O VAL C 201 " pdb=" CG2 VAL C 201 " model vdw 1.912 3.460 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.046 2.440 nonbonded pdb=" OG SER A 298 " pdb=" O GLY C 352 " model vdw 2.049 2.440 ... (remaining 76080 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: 2.850 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: 7.340 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.740 Find NCS groups from input model: 0.260 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:10.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.005 0.098 9038 Z= 0.309 Angle : 1.105 34.511 12242 Z= 0.714 Chirality : 0.084 1.297 1386 Planarity : 0.005 0.065 1548 Dihedral : 18.233 89.108 3198 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 5.37 % Allowed : 27.37 % Favored : 67.26 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 3.23 % 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: 0.12 (0.26), residues: 1118 helix: 1.55 (0.27), residues: 376 sheet: -0.03 (0.30), residues: 281 loop : -1.06 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.003 TRP A 91 HIS 0.010 0.001 HIS A 189 PHE 0.023 0.002 PHE A 276 TYR 0.111 0.003 TYR A 284 ARG 0.008 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 141 time to evaluate : 1.073 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 38 PHE cc_start: 0.6715 (t80) cc_final: 0.6493 (t80) REVERT: A 79 CYS cc_start: 0.7974 (m) cc_final: 0.7618 (m) REVERT: A 156 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7274 (mm) REVERT: A 258 LEU cc_start: 0.7171 (pp) cc_final: 0.6332 (mt) REVERT: C 309 ASP cc_start: 0.8273 (m-30) cc_final: 0.7952 (m-30) REVERT: B 46 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7630 (mpt180) outliers start: 51 outliers final: 43 residues processed: 185 average time/residue: 1.2222 time to fit residues: 241.0611 Evaluate side-chains 172 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 0.0370 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS A 86 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 HIS C 188 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.0530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9038 Z= 0.225 Angle : 0.555 6.204 12242 Z= 0.288 Chirality : 0.042 0.165 1386 Planarity : 0.004 0.050 1548 Dihedral : 7.982 59.650 1291 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.32 % Allowed : 25.05 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.26 (0.26), residues: 1118 helix: 1.76 (0.27), residues: 377 sheet: 0.05 (0.30), residues: 282 loop : -1.09 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.019 0.001 PHE A 38 TYR 0.013 0.001 TYR S 178 ARG 0.006 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 135 time to evaluate : 1.074 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 34 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.5199 (mp) REVERT: A 79 CYS cc_start: 0.7924 (m) cc_final: 0.7611 (m) REVERT: A 80 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6786 (mm) REVERT: A 110 ASN cc_start: 0.7752 (m-40) cc_final: 0.6964 (m-40) REVERT: A 258 LEU cc_start: 0.6990 (pp) cc_final: 0.6161 (mm) REVERT: C 318 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: B 46 ARG cc_start: 0.7999 (mtp-110) cc_final: 0.7623 (mpt180) REVERT: B 268 ASN cc_start: 0.7974 (t0) cc_final: 0.7570 (t0) outliers start: 60 outliers final: 25 residues processed: 175 average time/residue: 1.1626 time to fit residues: 217.4353 Evaluate side-chains 162 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9038 Z= 0.214 Angle : 0.539 6.967 12242 Z= 0.279 Chirality : 0.042 0.159 1386 Planarity : 0.004 0.044 1548 Dihedral : 6.507 58.293 1246 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.37 % Allowed : 26.84 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.31 (0.26), residues: 1118 helix: 1.90 (0.27), residues: 377 sheet: 0.02 (0.30), residues: 281 loop : -1.11 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.015 0.001 PHE C 189 TYR 0.014 0.001 TYR S 178 ARG 0.005 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 135 time to evaluate : 1.004 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7338 (tttt) cc_final: 0.6974 (mtpm) REVERT: A 34 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.5228 (mp) REVERT: A 79 CYS cc_start: 0.7938 (m) cc_final: 0.7675 (m) REVERT: A 80 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6773 (mm) REVERT: A 97 ASP cc_start: 0.5984 (OUTLIER) cc_final: 0.5491 (OUTLIER) REVERT: A 257 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6503 (mp) REVERT: A 258 LEU cc_start: 0.6929 (pp) cc_final: 0.6117 (mm) REVERT: C 309 ASP cc_start: 0.8277 (m-30) cc_final: 0.7961 (m-30) REVERT: B 46 ARG cc_start: 0.8003 (mtp-110) cc_final: 0.7659 (mpt180) REVERT: B 268 ASN cc_start: 0.7959 (t0) cc_final: 0.7557 (t0) outliers start: 51 outliers final: 25 residues processed: 170 average time/residue: 1.1223 time to fit residues: 204.3178 Evaluate side-chains 158 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.0970 chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 0.0980 chunk 107 optimal weight: 0.0870 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9038 Z= 0.177 Angle : 0.522 6.994 12242 Z= 0.270 Chirality : 0.041 0.154 1386 Planarity : 0.003 0.037 1548 Dihedral : 6.090 59.985 1241 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.84 % Allowed : 27.68 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.37 (0.26), residues: 1118 helix: 1.99 (0.27), residues: 377 sheet: 0.07 (0.30), residues: 280 loop : -1.12 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS B 225 PHE 0.022 0.001 PHE A 38 TYR 0.018 0.001 TYR A 269 ARG 0.006 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 137 time to evaluate : 1.085 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7282 (tttt) cc_final: 0.7012 (mtpm) REVERT: A 34 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.5092 (mp) REVERT: A 79 CYS cc_start: 0.8015 (m) cc_final: 0.7621 (m) REVERT: A 80 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6644 (mm) REVERT: A 94 LYS cc_start: 0.7174 (pptt) cc_final: 0.6201 (mmmt) REVERT: A 97 ASP cc_start: 0.6181 (OUTLIER) cc_final: 0.5878 (t0) REVERT: A 166 LYS cc_start: 0.5411 (tppt) cc_final: 0.5197 (tppp) REVERT: A 257 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6515 (mp) REVERT: A 258 LEU cc_start: 0.6899 (pp) cc_final: 0.6093 (mm) REVERT: C 350 ASP cc_start: 0.8158 (m-30) cc_final: 0.7939 (m-30) REVERT: B 46 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7704 (mpt180) REVERT: B 226 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: B 268 ASN cc_start: 0.7946 (t0) cc_final: 0.7554 (t0) REVERT: S 72 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.5715 (ptp90) outliers start: 46 outliers final: 21 residues processed: 174 average time/residue: 1.1672 time to fit residues: 217.4986 Evaluate side-chains 155 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.0770 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN C 188 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9038 Z= 0.366 Angle : 0.598 8.001 12242 Z= 0.309 Chirality : 0.045 0.205 1386 Planarity : 0.004 0.041 1548 Dihedral : 6.073 58.832 1237 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.58 % Allowed : 26.95 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.28 (0.26), residues: 1118 helix: 1.79 (0.27), residues: 382 sheet: 0.01 (0.30), residues: 298 loop : -1.11 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.017 0.002 PHE C 189 TYR 0.015 0.002 TYR A 269 ARG 0.007 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 128 time to evaluate : 1.100 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7317 (tttt) cc_final: 0.6947 (mtpm) REVERT: A 80 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6722 (mm) REVERT: A 97 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5518 (OUTLIER) REVERT: A 257 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6562 (mp) REVERT: A 258 LEU cc_start: 0.6890 (pp) cc_final: 0.6067 (mm) REVERT: C 318 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: B 46 ARG cc_start: 0.8055 (mtp-110) cc_final: 0.7695 (mpt180) REVERT: B 226 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: B 268 ASN cc_start: 0.7950 (t0) cc_final: 0.7572 (t0) REVERT: S 72 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.6069 (ptp90) outliers start: 53 outliers final: 26 residues processed: 165 average time/residue: 1.2238 time to fit residues: 215.5417 Evaluate side-chains 156 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN C 188 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9038 Z= 0.222 Angle : 0.555 8.636 12242 Z= 0.286 Chirality : 0.042 0.174 1386 Planarity : 0.004 0.039 1548 Dihedral : 5.614 56.325 1233 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.26 % Allowed : 28.21 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.29 (0.26), residues: 1118 helix: 1.88 (0.28), residues: 377 sheet: -0.04 (0.30), residues: 283 loop : -1.09 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS B 225 PHE 0.015 0.001 PHE C 189 TYR 0.014 0.001 TYR S 178 ARG 0.007 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 127 time to evaluate : 1.085 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7312 (tttt) cc_final: 0.6934 (mtpm) REVERT: A 80 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6765 (mm) REVERT: A 94 LYS cc_start: 0.7185 (pptt) cc_final: 0.6209 (mmmt) REVERT: A 257 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6563 (mp) REVERT: A 258 LEU cc_start: 0.6979 (pp) cc_final: 0.6199 (mm) REVERT: B 46 ARG cc_start: 0.8021 (mtp-110) cc_final: 0.7655 (mpt180) REVERT: B 70 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8911 (pp) REVERT: B 226 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: B 268 ASN cc_start: 0.7954 (t0) cc_final: 0.7546 (t0) REVERT: S 72 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.6148 (ptp90) outliers start: 50 outliers final: 27 residues processed: 164 average time/residue: 1.2241 time to fit residues: 214.4132 Evaluate side-chains 162 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.0020 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 175 ASN ** C 52 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** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9038 Z= 0.172 Angle : 0.545 9.071 12242 Z= 0.279 Chirality : 0.041 0.154 1386 Planarity : 0.003 0.037 1548 Dihedral : 5.436 56.293 1233 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.00 % Allowed : 29.26 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.33 (0.26), residues: 1118 helix: 1.97 (0.27), residues: 377 sheet: -0.07 (0.30), residues: 284 loop : -1.08 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS B 225 PHE 0.019 0.001 PHE A 38 TYR 0.014 0.001 TYR S 178 ARG 0.007 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 1.029 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7270 (tttt) cc_final: 0.6984 (mtpm) REVERT: A 79 CYS cc_start: 0.8018 (m) cc_final: 0.7630 (m) REVERT: A 80 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6714 (mm) REVERT: A 90 ARG cc_start: 0.6626 (mtp85) cc_final: 0.6391 (mtp85) REVERT: A 94 LYS cc_start: 0.7240 (pptt) cc_final: 0.6269 (mmmt) REVERT: A 227 LYS cc_start: 0.6351 (mmmm) cc_final: 0.6104 (mmmm) REVERT: A 257 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6521 (mp) REVERT: A 258 LEU cc_start: 0.6958 (pp) cc_final: 0.6187 (mm) REVERT: C 309 ASP cc_start: 0.8321 (m-30) cc_final: 0.8003 (m-30) REVERT: B 46 ARG cc_start: 0.8039 (mtp-110) cc_final: 0.7699 (mpt180) REVERT: B 215 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8016 (pp20) REVERT: B 226 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: B 268 ASN cc_start: 0.7956 (t0) cc_final: 0.7555 (t0) REVERT: S 72 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.6147 (ptp90) outliers start: 38 outliers final: 26 residues processed: 166 average time/residue: 1.1396 time to fit residues: 201.9348 Evaluate side-chains 160 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 0.2980 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 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** S 77 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9038 Z= 0.172 Angle : 0.546 8.093 12242 Z= 0.277 Chirality : 0.042 0.187 1386 Planarity : 0.004 0.037 1548 Dihedral : 5.301 56.342 1233 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.84 % Allowed : 28.42 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.36 (0.26), residues: 1118 helix: 1.98 (0.27), residues: 378 sheet: -0.08 (0.30), residues: 284 loop : -1.05 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.014 0.001 PHE C 189 TYR 0.012 0.001 TYR S 178 ARG 0.008 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 138 time to evaluate : 1.139 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7459 (tttt) cc_final: 0.7081 (mtpm) REVERT: A 79 CYS cc_start: 0.8000 (m) cc_final: 0.7701 (m) REVERT: A 80 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6645 (mm) REVERT: A 257 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6484 (mp) REVERT: A 258 LEU cc_start: 0.7095 (pp) cc_final: 0.6248 (mm) REVERT: C 309 ASP cc_start: 0.8323 (m-30) cc_final: 0.8026 (m-30) REVERT: B 46 ARG cc_start: 0.8043 (mtp-110) cc_final: 0.7708 (mpt180) REVERT: B 215 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7989 (pp20) REVERT: B 254 ASP cc_start: 0.8357 (t70) cc_final: 0.8073 (t0) REVERT: B 268 ASN cc_start: 0.7976 (t0) cc_final: 0.7576 (t0) REVERT: G 21 MET cc_start: 0.7527 (tpp) cc_final: 0.7198 (tpp) REVERT: S 180 MET cc_start: 0.8906 (ttp) cc_final: 0.8689 (tmm) outliers start: 46 outliers final: 26 residues processed: 172 average time/residue: 1.1568 time to fit residues: 212.7904 Evaluate side-chains 156 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.8980 chunk 60 optimal weight: 0.0770 chunk 43 optimal weight: 0.3980 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.0070 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** C 52 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** S 77 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9038 Z= 0.148 Angle : 0.553 11.060 12242 Z= 0.276 Chirality : 0.041 0.159 1386 Planarity : 0.003 0.036 1548 Dihedral : 4.988 56.882 1229 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.16 % Allowed : 29.68 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.49 (0.26), residues: 1118 helix: 2.13 (0.27), residues: 372 sheet: -0.03 (0.30), residues: 284 loop : -0.93 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.019 0.001 PHE A 38 TYR 0.013 0.001 TYR S 178 ARG 0.008 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.048 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7424 (tttt) cc_final: 0.7085 (mtpm) REVERT: A 80 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6623 (mm) REVERT: A 90 ARG cc_start: 0.6407 (mtp85) cc_final: 0.6173 (mtp85) REVERT: A 94 LYS cc_start: 0.7210 (pptt) cc_final: 0.6039 (mmmt) REVERT: A 257 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6404 (mp) REVERT: A 258 LEU cc_start: 0.7079 (pp) cc_final: 0.6232 (mm) REVERT: B 46 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7708 (mpt180) REVERT: B 215 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7953 (pp20) REVERT: B 254 ASP cc_start: 0.8251 (t70) cc_final: 0.8030 (t0) REVERT: B 268 ASN cc_start: 0.7975 (t0) cc_final: 0.7582 (t0) REVERT: G 21 MET cc_start: 0.7522 (tpp) cc_final: 0.7211 (tpp) outliers start: 30 outliers final: 23 residues processed: 159 average time/residue: 1.2271 time to fit residues: 208.3274 Evaluate side-chains 156 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 0.0570 chunk 101 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9038 Z= 0.148 Angle : 0.557 12.489 12242 Z= 0.276 Chirality : 0.041 0.158 1386 Planarity : 0.004 0.036 1548 Dihedral : 4.936 57.651 1229 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.95 % Allowed : 30.00 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.56 (0.26), residues: 1118 helix: 2.17 (0.27), residues: 372 sheet: 0.02 (0.30), residues: 282 loop : -0.88 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.013 0.001 PHE C 189 TYR 0.014 0.001 TYR S 178 ARG 0.009 0.000 ARG S 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 0.954 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7408 (tttt) cc_final: 0.7122 (mtpm) REVERT: A 80 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6419 (mm) REVERT: A 94 LYS cc_start: 0.7256 (pptt) cc_final: 0.6082 (mmmt) REVERT: A 232 PHE cc_start: 0.6721 (m-10) cc_final: 0.6440 (m-80) REVERT: A 257 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6428 (mp) REVERT: A 258 LEU cc_start: 0.7054 (pp) cc_final: 0.6199 (mm) REVERT: C 309 ASP cc_start: 0.8277 (m-30) cc_final: 0.7987 (m-30) REVERT: B 215 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7979 (pp20) REVERT: B 254 ASP cc_start: 0.8223 (t70) cc_final: 0.8009 (t0) REVERT: B 268 ASN cc_start: 0.7967 (t0) cc_final: 0.7577 (t0) REVERT: G 21 MET cc_start: 0.7497 (tpp) cc_final: 0.7203 (tpp) outliers start: 28 outliers final: 23 residues processed: 158 average time/residue: 1.1662 time to fit residues: 196.9004 Evaluate side-chains 154 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** C 52 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** S 77 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.150789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105767 restraints weight = 10408.466| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.34 r_work: 0.3080 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.195 9038 Z= 0.298 Angle : 0.892 59.198 12242 Z= 0.511 Chirality : 0.059 1.523 1386 Planarity : 0.004 0.051 1548 Dihedral : 4.755 57.650 1228 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.95 % Allowed : 29.89 % Favored : 67.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.23 % 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: 0.54 (0.26), residues: 1118 helix: 2.15 (0.27), residues: 372 sheet: 0.05 (0.30), residues: 282 loop : -0.92 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE C 189 TYR 0.013 0.001 TYR S 178 ARG 0.006 0.000 ARG S 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4166.20 seconds wall clock time: 74 minutes 21.63 seconds (4461.63 seconds total)