Starting phenix.real_space_refine on Fri Mar 15 01:10:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pt0_20470/03_2024/6pt0_20470_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pt0_20470/03_2024/6pt0_20470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pt0_20470/03_2024/6pt0_20470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pt0_20470/03_2024/6pt0_20470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pt0_20470/03_2024/6pt0_20470_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pt0_20470/03_2024/6pt0_20470_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.004 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 72 5.16 5 C 6554 2.51 5 N 1719 2.21 5 O 1887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 136": "NH1" <-> "NH2" Residue "R ARG 147": "NH1" <-> "NH2" Residue "R ARG 149": "NH1" <-> "NH2" Residue "R ARG 177": "NH1" <-> "NH2" Residue "R ARG 238": "NH1" <-> "NH2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 160": "NH1" <-> "NH2" 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: 10232 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2319 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "A" Number of atoms: 2824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2824 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 348} Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 216 Unusual residues: {'CLR': 4, 'PLM': 4, 'WI5': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 5.64, per 1000 atoms: 0.55 Number of scatterers: 10232 At special positions: 0 Unit cell: (91.581, 120.393, 136.857, 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 72 16.00 O 1887 8.00 N 1719 7.00 C 6554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " 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: 3.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 13 sheets defined 38.1% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'R' and resid 30 through 60 removed outlier: 4.140A pdb=" N ALA R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 66 Processing helix chain 'R' and resid 68 through 95 Processing helix chain 'R' and resid 103 through 136 Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 170 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 188 through 226 removed outlier: 3.935A pdb=" N HIS R 226 " --> pdb=" O SER R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 233 No H-bonds generated for 'chain 'R' and resid 230 through 233' Processing helix chain 'R' and resid 239 through 270 Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 275 through 301 Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 304 through 318 Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 64 through 87 removed outlier: 4.411A pdb=" N GLN A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.014A pdb=" N ASP A 103 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 112 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 115 " --> pdb=" O GLY A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 143 removed outlier: 4.088A pdb=" N PHE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 4.413A pdb=" N ALA A 153 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR A 154 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN A 157 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 171 through 180 removed outlier: 3.906A pdb=" N THR A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LYS A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.687A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.865A pdb=" N GLN A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.046A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 30 through 43 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 sheet with id= A, first strand: chain 'A' and resid 320 through 323 removed outlier: 4.200A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.892A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.414A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.699A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.867A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.422A 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: 6.631A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.544A 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: 6.640A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.696A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= K, first strand: chain 'E' and resid 49 through 51 Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.513A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 155 through 160 480 hydrogen bonds defined for protein. 1356 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: 2.40 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1647 1.31 - 1.44: 2814 1.44 - 1.57: 5883 1.57 - 1.70: 1 1.70 - 1.82: 105 Bond restraints: 10450 Sorted by residual: bond pdb=" C1 WI5 R 401 " pdb=" C2 WI5 R 401 " ideal model delta sigma weight residual 1.409 1.601 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" C23 WI5 R 401 " pdb=" C24 WI5 R 401 " ideal model delta sigma weight residual 1.366 1.516 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C12 WI5 R 401 " pdb=" C13 WI5 R 401 " ideal model delta sigma weight residual 1.380 1.529 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" C21 WI5 R 401 " pdb=" C22 WI5 R 401 " ideal model delta sigma weight residual 1.374 1.515 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C13 WI5 R 401 " pdb=" C8 WI5 R 401 " ideal model delta sigma weight residual 1.387 1.271 0.116 2.00e-02 2.50e+03 3.38e+01 ... (remaining 10445 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.14: 207 106.14 - 113.24: 5757 113.24 - 120.35: 3950 120.35 - 127.45: 4137 127.45 - 134.56: 98 Bond angle restraints: 14149 Sorted by residual: angle pdb=" C LYS A 180 " pdb=" N THR A 181 " pdb=" CA THR A 181 " ideal model delta sigma weight residual 121.54 129.96 -8.42 1.91e+00 2.74e-01 1.94e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.81e+01 angle pdb=" CA PRO R 138 " pdb=" C PRO R 138 " pdb=" N PRO R 139 " ideal model delta sigma weight residual 117.93 122.75 -4.82 1.20e+00 6.94e-01 1.61e+01 angle pdb=" C PRO E 41 " pdb=" N GLU E 42 " pdb=" CA GLU E 42 " ideal model delta sigma weight residual 121.54 128.91 -7.37 1.91e+00 2.74e-01 1.49e+01 angle pdb=" N PRO R 138 " pdb=" CA PRO R 138 " pdb=" C PRO R 138 " ideal model delta sigma weight residual 110.70 115.38 -4.68 1.22e+00 6.72e-01 1.47e+01 ... (remaining 14144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 6185 18.03 - 36.05: 193 36.05 - 54.08: 40 54.08 - 72.10: 4 72.10 - 90.13: 7 Dihedral angle restraints: 6429 sinusoidal: 2704 harmonic: 3725 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA THR B 86 " pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1418 0.085 - 0.170: 155 0.170 - 0.255: 17 0.255 - 0.340: 4 0.340 - 0.425: 5 Chirality restraints: 1599 Sorted by residual: chirality pdb=" C14 CLR R 406 " pdb=" C13 CLR R 406 " pdb=" C15 CLR R 406 " pdb=" C8 CLR R 406 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" C14 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C15 CLR R 404 " pdb=" C8 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CG LEU A 23 " pdb=" CB LEU A 23 " pdb=" CD1 LEU A 23 " pdb=" CD2 LEU A 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 1596 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 WI5 R 401 " -0.002 2.00e-02 2.50e+03 1.61e-02 7.13e+00 pdb=" C2 WI5 R 401 " -0.011 2.00e-02 2.50e+03 pdb=" C21 WI5 R 401 " -0.017 2.00e-02 2.50e+03 pdb=" C22 WI5 R 401 " -0.016 2.00e-02 2.50e+03 pdb=" C23 WI5 R 401 " -0.006 2.00e-02 2.50e+03 pdb=" C24 WI5 R 401 " -0.001 2.00e-02 2.50e+03 pdb=" C25 WI5 R 401 " 0.024 2.00e-02 2.50e+03 pdb=" C26 WI5 R 401 " 0.005 2.00e-02 2.50e+03 pdb=" C27 WI5 R 401 " -0.021 2.00e-02 2.50e+03 pdb=" C3 WI5 R 401 " 0.014 2.00e-02 2.50e+03 pdb=" C4 WI5 R 401 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO C 49 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 164 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C VAL R 164 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL R 164 " 0.013 2.00e-02 2.50e+03 pdb=" N SER R 165 " 0.011 2.00e-02 2.50e+03 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 979 2.76 - 3.29: 9747 3.29 - 3.83: 16799 3.83 - 4.36: 19223 4.36 - 4.90: 33569 Nonbonded interactions: 80317 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.222 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.270 2.440 nonbonded pdb=" O VAL R 164 " pdb=" OH TYR R 190 " model vdw 2.271 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.285 2.440 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.287 2.440 ... (remaining 80312 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: 0.290 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: 2.070 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.850 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 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 : 0.006 0.192 10450 Z= 0.387 Angle : 0.888 9.556 14149 Z= 0.454 Chirality : 0.060 0.425 1599 Planarity : 0.006 0.061 1761 Dihedral : 10.149 90.128 4023 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.20), residues: 1272 helix: -1.12 (0.18), residues: 507 sheet: -1.80 (0.28), residues: 275 loop : -1.90 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 111 HIS 0.008 0.001 HIS E 35 PHE 0.020 0.002 PHE A 189 TYR 0.029 0.002 TYR A 74 ARG 0.005 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 41 THR cc_start: 0.8831 (m) cc_final: 0.8475 (p) REVERT: R 56 TYR cc_start: 0.7524 (t80) cc_final: 0.7165 (t80) REVERT: R 65 ARG cc_start: 0.7497 (ttt180) cc_final: 0.6410 (mtm110) REVERT: R 130 ASP cc_start: 0.8801 (t70) cc_final: 0.8390 (t0) REVERT: R 146 THR cc_start: 0.7719 (m) cc_final: 0.7430 (p) REVERT: A 25 GLU cc_start: 0.8201 (tt0) cc_final: 0.7974 (tp30) REVERT: A 29 LYS cc_start: 0.8405 (ttmt) cc_final: 0.7997 (tptt) REVERT: A 224 CYS cc_start: 0.7694 (m) cc_final: 0.7475 (p) REVERT: A 330 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7992 (pttm) REVERT: A 333 GLN cc_start: 0.8506 (tp40) cc_final: 0.7971 (tp-100) REVERT: B 7 LEU cc_start: 0.9003 (mm) cc_final: 0.8757 (mm) REVERT: B 9 GLN cc_start: 0.9273 (mm110) cc_final: 0.8641 (tm-30) REVERT: B 10 GLU cc_start: 0.9468 (tp30) cc_final: 0.9180 (tp30) REVERT: B 32 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8474 (tm-30) REVERT: B 101 MET cc_start: 0.9139 (mtp) cc_final: 0.8812 (mtp) REVERT: B 209 LYS cc_start: 0.8673 (mttm) cc_final: 0.8327 (mttt) REVERT: B 243 THR cc_start: 0.8994 (m) cc_final: 0.8465 (p) REVERT: B 258 ASP cc_start: 0.8495 (t70) cc_final: 0.8282 (t0) REVERT: C 20 LYS cc_start: 0.9498 (ttpt) cc_final: 0.9127 (mtpp) REVERT: C 42 GLU cc_start: 0.8664 (tt0) cc_final: 0.8429 (tp30) REVERT: E 52 SER cc_start: 0.8625 (m) cc_final: 0.8084 (t) REVERT: E 73 ASP cc_start: 0.7224 (t70) cc_final: 0.6760 (t70) REVERT: E 80 PHE cc_start: 0.7823 (m-80) cc_final: 0.7555 (m-80) REVERT: E 223 ASP cc_start: 0.8605 (m-30) cc_final: 0.7126 (m-30) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.2755 time to fit residues: 129.5210 Evaluate side-chains 193 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 38 optimal weight: 0.0270 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 218 GLN R 226 HIS A 149 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10450 Z= 0.175 Angle : 0.588 8.450 14149 Z= 0.294 Chirality : 0.041 0.182 1599 Planarity : 0.004 0.040 1761 Dihedral : 6.315 54.426 1728 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.85 % Allowed : 13.60 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.91 (0.22), residues: 1272 helix: 0.77 (0.22), residues: 502 sheet: -1.53 (0.29), residues: 277 loop : -1.38 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.009 0.001 HIS B 54 PHE 0.018 0.001 PHE A 334 TYR 0.012 0.001 TYR R 207 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.5300 (tpt) REVERT: R 56 TYR cc_start: 0.7658 (t80) cc_final: 0.7238 (t80) REVERT: R 65 ARG cc_start: 0.7653 (ttt180) cc_final: 0.6629 (mtm110) REVERT: R 130 ASP cc_start: 0.8546 (t70) cc_final: 0.8334 (t0) REVERT: R 234 MET cc_start: 0.4473 (ppp) cc_final: 0.3565 (ppp) REVERT: R 275 ASP cc_start: 0.8394 (p0) cc_final: 0.7955 (p0) REVERT: R 283 PHE cc_start: 0.7524 (m-80) cc_final: 0.7276 (m-10) REVERT: R 292 SER cc_start: 0.8760 (m) cc_final: 0.8462 (p) REVERT: R 305 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 29 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7842 (tptt) REVERT: A 243 MET cc_start: 0.9481 (tpp) cc_final: 0.9241 (mmm) REVERT: A 330 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8154 (pttm) REVERT: B 10 GLU cc_start: 0.9522 (tp30) cc_final: 0.9196 (tp30) REVERT: B 101 MET cc_start: 0.9095 (mtp) cc_final: 0.8731 (mtp) REVERT: B 111 TYR cc_start: 0.8980 (m-80) cc_final: 0.8773 (m-80) REVERT: B 160 SER cc_start: 0.8825 (p) cc_final: 0.8553 (p) REVERT: B 211 TRP cc_start: 0.9001 (m100) cc_final: 0.8695 (m100) REVERT: B 243 THR cc_start: 0.8959 (m) cc_final: 0.8449 (p) REVERT: B 247 ASP cc_start: 0.7020 (t0) cc_final: 0.6738 (t70) REVERT: B 297 TRP cc_start: 0.8085 (m100) cc_final: 0.7882 (m100) REVERT: C 13 ARG cc_start: 0.9356 (mtt-85) cc_final: 0.8777 (ptp-110) REVERT: C 20 LYS cc_start: 0.9497 (ttpt) cc_final: 0.9151 (ptmm) REVERT: C 32 LYS cc_start: 0.9045 (tttt) cc_final: 0.8821 (tptp) REVERT: C 42 GLU cc_start: 0.8624 (tt0) cc_final: 0.8323 (tp30) REVERT: C 58 GLU cc_start: 0.8466 (pt0) cc_final: 0.7867 (pm20) REVERT: E 45 LEU cc_start: 0.8871 (mt) cc_final: 0.8632 (mt) REVERT: E 73 ASP cc_start: 0.7452 (t70) cc_final: 0.6563 (t70) REVERT: E 80 PHE cc_start: 0.7950 (m-80) cc_final: 0.7440 (m-80) REVERT: E 93 MET cc_start: 0.8456 (ttm) cc_final: 0.7756 (tpt) REVERT: E 148 PRO cc_start: 0.8822 (Cg_endo) cc_final: 0.8586 (Cg_exo) REVERT: E 220 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8434 (mp0) REVERT: E 223 ASP cc_start: 0.8388 (m-30) cc_final: 0.7148 (m-30) outliers start: 31 outliers final: 17 residues processed: 218 average time/residue: 0.2275 time to fit residues: 69.5400 Evaluate side-chains 192 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 239 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN E 39 GLN E 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10450 Z= 0.284 Angle : 0.600 9.805 14149 Z= 0.302 Chirality : 0.042 0.149 1599 Planarity : 0.004 0.052 1761 Dihedral : 6.142 56.226 1728 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.86 % Allowed : 14.43 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.25 (0.23), residues: 1272 helix: 1.38 (0.23), residues: 503 sheet: -1.15 (0.29), residues: 276 loop : -1.13 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 111 HIS 0.007 0.001 HIS E 232 PHE 0.015 0.001 PHE B 151 TYR 0.012 0.002 TYR R 132 ARG 0.008 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 178 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: R 23 LYS cc_start: 0.5915 (mptp) cc_final: 0.5511 (pttm) REVERT: R 26 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.5709 (tpt) REVERT: R 56 TYR cc_start: 0.7959 (t80) cc_final: 0.7460 (t80) REVERT: R 65 ARG cc_start: 0.7757 (ttt180) cc_final: 0.6796 (mtm110) REVERT: R 130 ASP cc_start: 0.8622 (t70) cc_final: 0.8353 (t0) REVERT: R 207 TYR cc_start: 0.7542 (t80) cc_final: 0.7142 (t80) REVERT: R 276 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8570 (pt0) REVERT: R 283 PHE cc_start: 0.7803 (m-80) cc_final: 0.7506 (m-10) REVERT: R 292 SER cc_start: 0.8872 (m) cc_final: 0.8536 (p) REVERT: R 313 CYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6960 (p) REVERT: A 29 LYS cc_start: 0.8399 (ttmt) cc_final: 0.7869 (tptt) REVERT: A 198 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7719 (ttp) REVERT: A 330 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8103 (ptmt) REVERT: B 7 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8603 (mm) REVERT: B 10 GLU cc_start: 0.9508 (tp30) cc_final: 0.9253 (tp30) REVERT: B 101 MET cc_start: 0.9011 (mtp) cc_final: 0.8650 (mtp) REVERT: B 130 GLU cc_start: 0.8215 (mp0) cc_final: 0.7954 (mp0) REVERT: B 160 SER cc_start: 0.8956 (p) cc_final: 0.8715 (p) REVERT: B 243 THR cc_start: 0.9120 (m) cc_final: 0.8613 (p) REVERT: C 13 ARG cc_start: 0.9372 (mtt-85) cc_final: 0.8815 (ptp-110) REVERT: C 20 LYS cc_start: 0.9537 (ttpt) cc_final: 0.9111 (ptmm) REVERT: C 29 LYS cc_start: 0.9102 (tppt) cc_final: 0.8493 (tppt) REVERT: C 32 LYS cc_start: 0.9225 (tttt) cc_final: 0.8921 (tptp) REVERT: C 36 ASP cc_start: 0.8779 (m-30) cc_final: 0.8091 (m-30) REVERT: C 58 GLU cc_start: 0.8566 (pt0) cc_final: 0.7969 (pm20) REVERT: E 51 ILE cc_start: 0.8152 (mp) cc_final: 0.7919 (mp) REVERT: E 73 ASP cc_start: 0.7623 (t70) cc_final: 0.6231 (t70) REVERT: E 93 MET cc_start: 0.8520 (ttm) cc_final: 0.7925 (tpt) REVERT: E 140 MET cc_start: 0.9052 (mmm) cc_final: 0.8011 (mmm) REVERT: E 178 LEU cc_start: 0.9198 (tp) cc_final: 0.8910 (tp) REVERT: E 220 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8213 (mp0) REVERT: E 223 ASP cc_start: 0.8451 (m-30) cc_final: 0.6938 (m-30) outliers start: 42 outliers final: 25 residues processed: 206 average time/residue: 0.2214 time to fit residues: 64.1289 Evaluate side-chains 189 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 313 CYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 0.3980 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10450 Z= 0.263 Angle : 0.575 10.176 14149 Z= 0.291 Chirality : 0.041 0.150 1599 Planarity : 0.004 0.050 1761 Dihedral : 6.076 56.539 1728 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.40 % Allowed : 15.44 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.08 (0.24), residues: 1272 helix: 1.69 (0.23), residues: 502 sheet: -0.97 (0.30), residues: 279 loop : -1.00 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.006 0.001 HIS E 232 PHE 0.012 0.001 PHE B 151 TYR 0.014 0.001 TYR B 59 ARG 0.006 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 169 time to evaluate : 1.165 Fit side-chains REVERT: R 23 LYS cc_start: 0.6088 (mptp) cc_final: 0.5627 (pttm) REVERT: R 42 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8335 (mm) REVERT: R 56 TYR cc_start: 0.8052 (t80) cc_final: 0.7493 (t80) REVERT: R 65 ARG cc_start: 0.7796 (ttt180) cc_final: 0.6872 (mtm110) REVERT: R 130 ASP cc_start: 0.8522 (t70) cc_final: 0.8265 (t0) REVERT: R 207 TYR cc_start: 0.7614 (t80) cc_final: 0.7054 (t80) REVERT: R 276 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8243 (pt0) REVERT: R 283 PHE cc_start: 0.7774 (m-80) cc_final: 0.7561 (m-10) REVERT: R 292 SER cc_start: 0.8966 (m) cc_final: 0.8602 (p) REVERT: R 313 CYS cc_start: 0.7481 (t) cc_final: 0.6979 (p) REVERT: A 224 CYS cc_start: 0.8483 (m) cc_final: 0.7636 (p) REVERT: A 330 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8286 (ptmt) REVERT: B 7 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8615 (mm) REVERT: B 10 GLU cc_start: 0.9504 (tp30) cc_final: 0.9283 (tp30) REVERT: B 101 MET cc_start: 0.8978 (mtp) cc_final: 0.8659 (mtp) REVERT: B 160 SER cc_start: 0.8935 (p) cc_final: 0.8721 (p) REVERT: B 217 MET cc_start: 0.8093 (ppp) cc_final: 0.7700 (ppp) REVERT: B 243 THR cc_start: 0.9148 (m) cc_final: 0.8632 (p) REVERT: B 297 TRP cc_start: 0.8925 (m100) cc_final: 0.8310 (m100) REVERT: C 20 LYS cc_start: 0.9505 (ttpt) cc_final: 0.9064 (ptmm) REVERT: C 29 LYS cc_start: 0.9158 (tppt) cc_final: 0.8594 (mmmt) REVERT: C 30 VAL cc_start: 0.9211 (t) cc_final: 0.8988 (t) REVERT: C 58 GLU cc_start: 0.8575 (pt0) cc_final: 0.8107 (pm20) REVERT: E 73 ASP cc_start: 0.7433 (t70) cc_final: 0.6833 (t70) REVERT: E 93 MET cc_start: 0.8464 (ttm) cc_final: 0.7891 (tpt) REVERT: E 140 MET cc_start: 0.9167 (mmm) cc_final: 0.8199 (mmm) REVERT: E 223 ASP cc_start: 0.8481 (m-30) cc_final: 0.7928 (m-30) outliers start: 37 outliers final: 21 residues processed: 194 average time/residue: 0.2120 time to fit residues: 57.7889 Evaluate side-chains 184 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10450 Z= 0.181 Angle : 0.537 7.581 14149 Z= 0.271 Chirality : 0.040 0.166 1599 Planarity : 0.003 0.039 1761 Dihedral : 5.922 58.815 1728 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.85 % Allowed : 16.82 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.26 (0.24), residues: 1272 helix: 1.74 (0.23), residues: 508 sheet: -0.81 (0.30), residues: 277 loop : -0.85 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS E 232 PHE 0.011 0.001 PHE B 278 TYR 0.014 0.001 TYR B 59 ARG 0.007 0.000 ARG R 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.269 Fit side-chains REVERT: R 56 TYR cc_start: 0.8056 (t80) cc_final: 0.7487 (t80) REVERT: R 62 HIS cc_start: 0.6853 (p-80) cc_final: 0.6275 (p-80) REVERT: R 65 ARG cc_start: 0.7849 (ttt180) cc_final: 0.6869 (mtm110) REVERT: R 130 ASP cc_start: 0.8448 (t70) cc_final: 0.8236 (t0) REVERT: R 207 TYR cc_start: 0.7610 (t80) cc_final: 0.7258 (t80) REVERT: R 276 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8297 (pt0) REVERT: R 292 SER cc_start: 0.8963 (m) cc_final: 0.8611 (p) REVERT: R 313 CYS cc_start: 0.7377 (t) cc_final: 0.6979 (p) REVERT: A 330 LYS cc_start: 0.8613 (mmtt) cc_final: 0.8283 (ptmt) REVERT: B 7 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8615 (mm) REVERT: B 10 GLU cc_start: 0.9529 (tp30) cc_final: 0.9188 (tp30) REVERT: B 101 MET cc_start: 0.8883 (mtp) cc_final: 0.8556 (mtp) REVERT: B 217 MET cc_start: 0.8140 (ppp) cc_final: 0.7702 (ppp) REVERT: B 243 THR cc_start: 0.9122 (m) cc_final: 0.8773 (p) REVERT: B 297 TRP cc_start: 0.8868 (m100) cc_final: 0.7825 (m100) REVERT: C 16 VAL cc_start: 0.9262 (t) cc_final: 0.8964 (m) REVERT: C 20 LYS cc_start: 0.9451 (ttpt) cc_final: 0.9106 (ptmm) REVERT: C 29 LYS cc_start: 0.9191 (tppt) cc_final: 0.8623 (mmmt) REVERT: C 30 VAL cc_start: 0.9252 (t) cc_final: 0.9016 (t) REVERT: C 58 GLU cc_start: 0.8588 (pt0) cc_final: 0.8125 (pm20) REVERT: E 11 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7428 (mm) REVERT: E 51 ILE cc_start: 0.8129 (mp) cc_final: 0.7842 (mp) REVERT: E 73 ASP cc_start: 0.7492 (t70) cc_final: 0.6891 (t70) REVERT: E 83 MET cc_start: 0.8582 (mtm) cc_final: 0.8292 (mtm) REVERT: E 93 MET cc_start: 0.8427 (ttm) cc_final: 0.7906 (tpt) REVERT: E 140 MET cc_start: 0.9147 (mmm) cc_final: 0.8228 (mmm) REVERT: E 220 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7901 (mp0) REVERT: E 223 ASP cc_start: 0.8491 (m-30) cc_final: 0.7231 (m-30) REVERT: E 244 LYS cc_start: 0.8509 (ttmm) cc_final: 0.7990 (ttpp) outliers start: 31 outliers final: 23 residues processed: 191 average time/residue: 0.2073 time to fit residues: 56.9688 Evaluate side-chains 187 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.4980 chunk 110 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 102 optimal weight: 0.0170 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 0.2980 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10450 Z= 0.178 Angle : 0.538 7.701 14149 Z= 0.269 Chirality : 0.040 0.148 1599 Planarity : 0.003 0.039 1761 Dihedral : 5.907 57.597 1728 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.58 % Allowed : 16.91 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.24), residues: 1272 helix: 1.92 (0.23), residues: 501 sheet: -0.64 (0.31), residues: 271 loop : -0.96 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS E 232 PHE 0.011 0.001 PHE B 292 TYR 0.012 0.001 TYR B 59 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.116 Fit side-chains REVERT: R 56 TYR cc_start: 0.8070 (t80) cc_final: 0.7502 (t80) REVERT: R 65 ARG cc_start: 0.7863 (ttt180) cc_final: 0.6832 (mtm110) REVERT: R 130 ASP cc_start: 0.8412 (t70) cc_final: 0.8185 (t0) REVERT: R 146 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7597 (p) REVERT: R 207 TYR cc_start: 0.7559 (t80) cc_final: 0.7022 (t80) REVERT: R 276 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8279 (pt0) REVERT: R 292 SER cc_start: 0.8973 (m) cc_final: 0.8612 (p) REVERT: R 313 CYS cc_start: 0.7403 (t) cc_final: 0.7082 (p) REVERT: A 106 GLN cc_start: 0.6470 (mm110) cc_final: 0.6047 (mm110) REVERT: A 330 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8290 (ptmt) REVERT: B 7 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8621 (mm) REVERT: B 10 GLU cc_start: 0.9522 (tp30) cc_final: 0.9300 (tp30) REVERT: B 101 MET cc_start: 0.8874 (mtp) cc_final: 0.8597 (mtp) REVERT: B 228 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7694 (p0) REVERT: B 243 THR cc_start: 0.9137 (m) cc_final: 0.8822 (p) REVERT: B 297 TRP cc_start: 0.8871 (m100) cc_final: 0.7865 (m100) REVERT: C 16 VAL cc_start: 0.9275 (t) cc_final: 0.9035 (m) REVERT: C 20 LYS cc_start: 0.9510 (ttpt) cc_final: 0.9051 (ptmm) REVERT: C 29 LYS cc_start: 0.9165 (tppt) cc_final: 0.8746 (mmmt) REVERT: C 58 GLU cc_start: 0.8586 (pt0) cc_final: 0.8133 (pm20) REVERT: E 11 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7425 (mm) REVERT: E 73 ASP cc_start: 0.7490 (t70) cc_final: 0.6899 (t70) REVERT: E 83 MET cc_start: 0.8606 (mtm) cc_final: 0.8303 (mtm) REVERT: E 93 MET cc_start: 0.8436 (ttm) cc_final: 0.7907 (tpt) REVERT: E 220 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8153 (mp0) REVERT: E 223 ASP cc_start: 0.8262 (m-30) cc_final: 0.6883 (m-30) REVERT: E 231 GLN cc_start: 0.8911 (pp30) cc_final: 0.8681 (pp30) REVERT: E 244 LYS cc_start: 0.8393 (ttmm) cc_final: 0.7945 (ttpp) outliers start: 39 outliers final: 25 residues processed: 192 average time/residue: 0.2018 time to fit residues: 55.4127 Evaluate side-chains 184 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10450 Z= 0.188 Angle : 0.541 7.095 14149 Z= 0.269 Chirality : 0.040 0.172 1599 Planarity : 0.003 0.039 1761 Dihedral : 5.859 58.246 1728 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.22 % Allowed : 17.10 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.42 (0.24), residues: 1272 helix: 1.97 (0.23), residues: 501 sheet: -0.57 (0.31), residues: 272 loop : -0.96 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS E 232 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR B 59 ARG 0.006 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6443 (tpp) cc_final: 0.6133 (tpp) REVERT: R 56 TYR cc_start: 0.8078 (t80) cc_final: 0.7485 (t80) REVERT: R 65 ARG cc_start: 0.7843 (ttt180) cc_final: 0.6828 (mtm110) REVERT: R 130 ASP cc_start: 0.8392 (t70) cc_final: 0.8168 (t0) REVERT: R 146 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7601 (p) REVERT: R 207 TYR cc_start: 0.7699 (t80) cc_final: 0.7087 (t80) REVERT: R 276 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8266 (pt0) REVERT: R 292 SER cc_start: 0.9017 (m) cc_final: 0.8670 (p) REVERT: R 313 CYS cc_start: 0.7394 (t) cc_final: 0.7066 (p) REVERT: A 106 GLN cc_start: 0.6583 (mm110) cc_final: 0.6184 (mm110) REVERT: A 330 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8297 (ptmt) REVERT: B 101 MET cc_start: 0.8878 (mtp) cc_final: 0.8590 (mtp) REVERT: B 228 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7629 (p0) REVERT: B 243 THR cc_start: 0.9136 (m) cc_final: 0.8817 (p) REVERT: B 339 TRP cc_start: 0.8823 (m100) cc_final: 0.8371 (m100) REVERT: C 29 LYS cc_start: 0.9168 (tppt) cc_final: 0.8548 (mmmt) REVERT: C 58 GLU cc_start: 0.8577 (pt0) cc_final: 0.8110 (pm20) REVERT: E 11 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7400 (mm) REVERT: E 51 ILE cc_start: 0.7867 (mp) cc_final: 0.7572 (tt) REVERT: E 73 ASP cc_start: 0.7563 (t70) cc_final: 0.6982 (t70) REVERT: E 83 MET cc_start: 0.8627 (mtm) cc_final: 0.8356 (mtm) REVERT: E 93 MET cc_start: 0.8456 (ttm) cc_final: 0.7935 (tpt) REVERT: E 220 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8161 (mp0) REVERT: E 223 ASP cc_start: 0.8171 (m-30) cc_final: 0.6648 (m-30) REVERT: E 231 GLN cc_start: 0.8891 (pp30) cc_final: 0.8640 (pp30) REVERT: E 244 LYS cc_start: 0.8445 (ttmm) cc_final: 0.7982 (ttpp) outliers start: 35 outliers final: 23 residues processed: 183 average time/residue: 0.2170 time to fit residues: 56.2424 Evaluate side-chains 182 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 194 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 60 optimal weight: 0.0020 chunk 11 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10450 Z= 0.151 Angle : 0.543 8.416 14149 Z= 0.270 Chirality : 0.040 0.164 1599 Planarity : 0.003 0.040 1761 Dihedral : 5.745 58.579 1728 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.57 % Allowed : 17.92 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.44 (0.24), residues: 1272 helix: 1.94 (0.23), residues: 501 sheet: -0.47 (0.30), residues: 280 loop : -0.96 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.002 0.000 HIS E 232 PHE 0.009 0.001 PHE A 189 TYR 0.010 0.001 TYR B 59 ARG 0.006 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 56 TYR cc_start: 0.8072 (t80) cc_final: 0.7476 (t80) REVERT: R 65 ARG cc_start: 0.7822 (ttt180) cc_final: 0.6801 (mtm110) REVERT: R 130 ASP cc_start: 0.8328 (t70) cc_final: 0.8107 (t0) REVERT: R 146 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7674 (p) REVERT: R 207 TYR cc_start: 0.7696 (t80) cc_final: 0.7024 (t80) REVERT: R 239 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7271 (pp) REVERT: R 276 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8272 (pt0) REVERT: R 292 SER cc_start: 0.9070 (m) cc_final: 0.8708 (p) REVERT: R 313 CYS cc_start: 0.7337 (t) cc_final: 0.7023 (p) REVERT: A 106 GLN cc_start: 0.6483 (mm110) cc_final: 0.6100 (mm110) REVERT: A 224 CYS cc_start: 0.8344 (m) cc_final: 0.7682 (p) REVERT: A 330 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8315 (ptmt) REVERT: B 101 MET cc_start: 0.8830 (mtp) cc_final: 0.8551 (mtp) REVERT: B 207 SER cc_start: 0.8795 (m) cc_final: 0.8314 (p) REVERT: B 228 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7685 (p0) REVERT: B 243 THR cc_start: 0.9123 (m) cc_final: 0.8853 (p) REVERT: C 20 LYS cc_start: 0.9331 (ttmm) cc_final: 0.8969 (mtpp) REVERT: C 29 LYS cc_start: 0.9130 (tppt) cc_final: 0.8552 (mmmt) REVERT: C 58 GLU cc_start: 0.8581 (pt0) cc_final: 0.8099 (pm20) REVERT: E 11 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7393 (mm) REVERT: E 13 GLN cc_start: 0.8040 (pm20) cc_final: 0.7755 (pm20) REVERT: E 51 ILE cc_start: 0.7901 (mp) cc_final: 0.7607 (tt) REVERT: E 73 ASP cc_start: 0.7531 (t70) cc_final: 0.6948 (t70) REVERT: E 93 MET cc_start: 0.8422 (ttm) cc_final: 0.7926 (tpt) REVERT: E 220 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8041 (mp0) REVERT: E 223 ASP cc_start: 0.8283 (m-30) cc_final: 0.6437 (m-30) REVERT: E 244 LYS cc_start: 0.8474 (ttmm) cc_final: 0.7936 (ttpp) outliers start: 28 outliers final: 18 residues processed: 186 average time/residue: 0.2092 time to fit residues: 55.8790 Evaluate side-chains 181 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 103 optimal weight: 0.0270 chunk 107 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10450 Z= 0.158 Angle : 0.556 9.364 14149 Z= 0.274 Chirality : 0.040 0.172 1599 Planarity : 0.003 0.040 1761 Dihedral : 5.695 59.344 1728 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.67 % Allowed : 18.20 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.46 (0.24), residues: 1272 helix: 1.96 (0.23), residues: 503 sheet: -0.50 (0.30), residues: 283 loop : -0.92 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.000 HIS E 232 PHE 0.010 0.001 PHE A 189 TYR 0.015 0.001 TYR A 287 ARG 0.004 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.320 Fit side-chains REVERT: R 56 TYR cc_start: 0.8067 (t80) cc_final: 0.7483 (t80) REVERT: R 65 ARG cc_start: 0.7765 (ttt180) cc_final: 0.6830 (mtm110) REVERT: R 130 ASP cc_start: 0.8346 (t70) cc_final: 0.8096 (t0) REVERT: R 146 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7679 (p) REVERT: R 207 TYR cc_start: 0.7686 (t80) cc_final: 0.7008 (t80) REVERT: R 313 CYS cc_start: 0.7320 (t) cc_final: 0.7032 (p) REVERT: A 106 GLN cc_start: 0.6486 (mm110) cc_final: 0.6114 (mm110) REVERT: A 330 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8324 (ptmt) REVERT: B 101 MET cc_start: 0.8782 (mtp) cc_final: 0.8519 (mtp) REVERT: B 207 SER cc_start: 0.8777 (m) cc_final: 0.8323 (p) REVERT: B 228 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7707 (p0) REVERT: B 243 THR cc_start: 0.9154 (m) cc_final: 0.8922 (p) REVERT: B 297 TRP cc_start: 0.8818 (m100) cc_final: 0.7901 (m100) REVERT: B 339 TRP cc_start: 0.8706 (m100) cc_final: 0.8312 (m100) REVERT: C 20 LYS cc_start: 0.9395 (ttmm) cc_final: 0.8888 (mtpp) REVERT: C 29 LYS cc_start: 0.9082 (tppt) cc_final: 0.8687 (mmmt) REVERT: C 58 GLU cc_start: 0.8593 (pt0) cc_final: 0.8122 (pm20) REVERT: E 11 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7367 (mm) REVERT: E 13 GLN cc_start: 0.8074 (pm20) cc_final: 0.7789 (pm20) REVERT: E 51 ILE cc_start: 0.7899 (mp) cc_final: 0.7653 (tt) REVERT: E 73 ASP cc_start: 0.7537 (t70) cc_final: 0.6951 (t70) REVERT: E 93 MET cc_start: 0.8427 (ttm) cc_final: 0.7933 (tpt) REVERT: E 220 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8051 (mp0) REVERT: E 223 ASP cc_start: 0.8273 (m-30) cc_final: 0.6402 (m-30) REVERT: E 244 LYS cc_start: 0.8471 (ttmm) cc_final: 0.7939 (ttpp) outliers start: 29 outliers final: 23 residues processed: 179 average time/residue: 0.2172 time to fit residues: 55.2898 Evaluate side-chains 179 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 295 ASN Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 57 optimal weight: 0.0670 chunk 83 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 77 optimal weight: 0.0370 chunk 61 optimal weight: 4.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 98 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10450 Z= 0.248 Angle : 0.606 9.115 14149 Z= 0.299 Chirality : 0.042 0.211 1599 Planarity : 0.003 0.041 1761 Dihedral : 5.883 60.281 1728 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.94 % Allowed : 18.01 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.40 (0.24), residues: 1272 helix: 1.89 (0.23), residues: 501 sheet: -0.46 (0.31), residues: 263 loop : -0.96 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 339 HIS 0.005 0.001 HIS E 232 PHE 0.014 0.001 PHE B 292 TYR 0.015 0.001 TYR A 287 ARG 0.005 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: R 56 TYR cc_start: 0.8119 (t80) cc_final: 0.7706 (t80) REVERT: R 65 ARG cc_start: 0.7860 (ttt180) cc_final: 0.6956 (mtm110) REVERT: R 130 ASP cc_start: 0.8480 (t70) cc_final: 0.8254 (t0) REVERT: R 146 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7748 (p) REVERT: R 207 TYR cc_start: 0.7722 (t80) cc_final: 0.7056 (t80) REVERT: R 313 CYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7004 (p) REVERT: A 106 GLN cc_start: 0.6596 (mm110) cc_final: 0.6211 (mm110) REVERT: A 330 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8340 (ptmt) REVERT: B 101 MET cc_start: 0.8918 (mtp) cc_final: 0.8616 (mtp) REVERT: B 207 SER cc_start: 0.8717 (m) cc_final: 0.8273 (p) REVERT: B 215 GLU cc_start: 0.8441 (mp0) cc_final: 0.8240 (mp0) REVERT: B 228 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7573 (p0) REVERT: B 243 THR cc_start: 0.9193 (m) cc_final: 0.8742 (p) REVERT: C 20 LYS cc_start: 0.9402 (ttmm) cc_final: 0.8944 (mtpp) REVERT: C 58 GLU cc_start: 0.8549 (pt0) cc_final: 0.8065 (pm20) REVERT: E 11 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7315 (mm) REVERT: E 13 GLN cc_start: 0.8093 (pm20) cc_final: 0.7831 (pm20) REVERT: E 51 ILE cc_start: 0.7916 (mp) cc_final: 0.7687 (tt) REVERT: E 73 ASP cc_start: 0.7622 (t70) cc_final: 0.6827 (t70) REVERT: E 76 LYS cc_start: 0.8933 (mtmm) cc_final: 0.8560 (mtmm) REVERT: E 93 MET cc_start: 0.8492 (ttm) cc_final: 0.7839 (tpt) REVERT: E 220 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8068 (mp0) REVERT: E 223 ASP cc_start: 0.8220 (m-30) cc_final: 0.6319 (m-30) outliers start: 32 outliers final: 25 residues processed: 174 average time/residue: 0.2130 time to fit residues: 52.7584 Evaluate side-chains 179 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 295 ASN Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain R residue 313 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 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 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 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 = 0.3922 r_free = 0.3922 target = 0.125882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.082437 restraints weight = 19839.377| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.30 r_work: 0.3022 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10450 Z= 0.217 Angle : 0.604 9.833 14149 Z= 0.296 Chirality : 0.041 0.211 1599 Planarity : 0.003 0.041 1761 Dihedral : 5.899 60.134 1728 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.94 % Allowed : 17.83 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.41 (0.24), residues: 1272 helix: 1.93 (0.23), residues: 500 sheet: -0.57 (0.30), residues: 285 loop : -0.92 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.004 0.001 HIS E 232 PHE 0.014 0.001 PHE E 68 TYR 0.025 0.001 TYR C 40 ARG 0.004 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.51 seconds wall clock time: 46 minutes 11.05 seconds (2771.05 seconds total)