Starting phenix.real_space_refine on Wed Feb 14 15:47:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vl9_32021/02_2024/7vl9_32021_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vl9_32021/02_2024/7vl9_32021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vl9_32021/02_2024/7vl9_32021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vl9_32021/02_2024/7vl9_32021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vl9_32021/02_2024/7vl9_32021_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vl9_32021/02_2024/7vl9_32021_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 68 5.16 5 C 6152 2.51 5 N 1616 2.21 5 O 1769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "R PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 306": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9605 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "L" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 496 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "R" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2493 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "S" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.22, per 1000 atoms: 0.54 Number of scatterers: 9605 At special positions: 0 Unit cell: (110.313, 134.946, 126.378, 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 68 16.00 O 1769 8.00 N 1616 7.00 C 6152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS L 32 " - pdb=" SG CYS L 56 " distance=2.03 Simple disulfide: pdb=" SG CYS L 33 " - pdb=" SG CYS L 72 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 83 " distance=2.03 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 273 " distance=2.04 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 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: 3.64 Conformation dependent library (CDL) restraints added in 1.8 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 15 sheets defined 34.6% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.527A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.256A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.941A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.715A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'L' and resid 43 through 45 No H-bonds generated for 'chain 'L' and resid 43 through 45' Processing helix chain 'L' and resid 78 through 86 removed outlier: 4.623A pdb=" N ASP L 82 " --> pdb=" O PRO L 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 58 Proline residue: R 38 - end of helix removed outlier: 3.775A pdb=" N VAL R 46 " --> pdb=" O SER R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 96 removed outlier: 4.112A pdb=" N THR R 86 " --> pdb=" O LEU R 82 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU R 87 " --> pdb=" O PHE R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 Processing helix chain 'R' and resid 140 through 142 No H-bonds generated for 'chain 'R' and resid 140 through 142' Processing helix chain 'R' and resid 147 through 171 removed outlier: 3.514A pdb=" N MET R 166 " --> pdb=" O ILE R 162 " (cutoff:3.500A) Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 192 through 205 removed outlier: 3.647A pdb=" N LEU R 203 " --> pdb=" O GLN R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 227 removed outlier: 3.876A pdb=" N GLY R 221 " --> pdb=" O ILE R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 263 Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 265 through 268 No H-bonds generated for 'chain 'R' and resid 265 through 268' Processing helix chain 'R' and resid 275 through 301 removed outlier: 3.577A pdb=" N ILE R 289 " --> pdb=" O VAL R 285 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 306 through 317 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.455A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.917A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.019A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.702A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.091A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.164A 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: 6.684A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.990A 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: 6.501A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.343A 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: 6.583A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 71 through 73 Processing sheet with id= J, first strand: chain 'R' and resid 173 through 177 Processing sheet with id= K, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.005A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.756A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= O, first strand: chain 'S' and resid 226 through 231 removed outlier: 3.617A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 433 hydrogen bonds defined for protein. 1236 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: 2.73 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1715 1.32 - 1.45: 2785 1.45 - 1.58: 5219 1.58 - 1.71: 2 1.71 - 1.84: 96 Bond restraints: 9817 Sorted by residual: bond pdb=" CA ILE S 100 " pdb=" C ILE S 100 " ideal model delta sigma weight residual 1.522 1.458 0.063 1.22e-02 6.72e+03 2.70e+01 bond pdb=" CA GLN S 82 " pdb=" C GLN S 82 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.20e-02 6.94e+03 2.44e+01 bond pdb=" CA LYS L 66 " pdb=" C LYS L 66 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.32e-02 5.74e+03 2.08e+01 bond pdb=" CA LEU R 192 " pdb=" C LEU R 192 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.27e-02 6.20e+03 2.07e+01 bond pdb=" CA THR B 47 " pdb=" C THR B 47 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.33e-02 5.65e+03 1.51e+01 ... (remaining 9812 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.48: 164 105.48 - 112.71: 5118 112.71 - 119.94: 3443 119.94 - 127.17: 4459 127.17 - 134.40: 106 Bond angle restraints: 13290 Sorted by residual: angle pdb=" N ASP B 205 " pdb=" CA ASP B 205 " pdb=" C ASP B 205 " ideal model delta sigma weight residual 112.88 103.30 9.58 1.29e+00 6.01e-01 5.52e+01 angle pdb=" N GLY L 68 " pdb=" CA GLY L 68 " pdb=" C GLY L 68 " ideal model delta sigma weight residual 115.21 124.60 -9.39 1.30e+00 5.92e-01 5.22e+01 angle pdb=" N LEU R 197 " pdb=" CA LEU R 197 " pdb=" C LEU R 197 " ideal model delta sigma weight residual 111.07 103.83 7.24 1.07e+00 8.73e-01 4.57e+01 angle pdb=" N LYS L 66 " pdb=" CA LYS L 66 " pdb=" C LYS L 66 " ideal model delta sigma weight residual 111.69 103.45 8.24 1.23e+00 6.61e-01 4.48e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 112.59 104.44 8.15 1.22e+00 6.72e-01 4.46e+01 ... (remaining 13285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5389 17.96 - 35.91: 403 35.91 - 53.87: 67 53.87 - 71.82: 19 71.82 - 89.78: 7 Dihedral angle restraints: 5885 sinusoidal: 2359 harmonic: 3526 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 3.86 89.14 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual -86.00 -168.72 82.72 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CB CYS L 32 " pdb=" SG CYS L 32 " pdb=" SG CYS L 56 " pdb=" CB CYS L 56 " ideal model delta sinusoidal sigma weight residual 93.00 147.84 -54.84 1 1.00e+01 1.00e-02 4.07e+01 ... (remaining 5882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1316 0.089 - 0.178: 159 0.178 - 0.267: 15 0.267 - 0.356: 5 0.356 - 0.445: 6 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA ASN S 77 " pdb=" N ASN S 77 " pdb=" C ASN S 77 " pdb=" CB ASN S 77 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA THR B 164 " pdb=" N THR B 164 " pdb=" C THR B 164 " pdb=" CB THR B 164 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1498 not shown) Planarity restraints: 1667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR S 190 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C TYR S 190 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR S 190 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG S 191 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " -0.015 2.00e-02 2.50e+03 1.38e-02 4.78e+00 pdb=" CG TRP B 63 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO S 107 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.030 5.00e-02 4.00e+02 ... (remaining 1664 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 503 2.72 - 3.27: 9532 3.27 - 3.81: 15758 3.81 - 4.36: 20123 4.36 - 4.90: 34329 Nonbonded interactions: 80245 Sorted by model distance: nonbonded pdb=" O PHE R 178 " pdb=" OG1 THR R 179 " model vdw 2.176 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.213 2.440 nonbonded pdb=" O MET S 192 " pdb=" OG SER S 193 " model vdw 2.216 2.440 nonbonded pdb=" O GLY B 224 " pdb=" NH1 ARG B 251 " model vdw 2.222 2.520 nonbonded pdb=" OE2 GLU L 51 " pdb=" NE2 GLN R 175 " model vdw 2.251 2.520 ... (remaining 80240 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: 0.780 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: 2.860 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.010 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.007 0.063 9817 Z= 0.443 Angle : 0.955 11.358 13290 Z= 0.573 Chirality : 0.064 0.445 1501 Planarity : 0.005 0.054 1667 Dihedral : 13.152 89.775 3590 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.10 % Allowed : 1.43 % Favored : 98.48 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.78 % 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: 0.32 (0.24), residues: 1196 helix: 1.01 (0.25), residues: 414 sheet: 0.80 (0.30), residues: 279 loop : -0.76 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 63 HIS 0.008 0.002 HIS B 91 PHE 0.030 0.003 PHE S 212 TYR 0.034 0.003 TYR S 175 ARG 0.030 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8022 (tptp) cc_final: 0.7581 (OUTLIER) REVERT: B 129 ARG cc_start: 0.7324 (ttt180) cc_final: 0.7023 (tpt90) REVERT: B 245 SER cc_start: 0.8329 (p) cc_final: 0.8105 (p) REVERT: S 80 PHE cc_start: 0.8260 (m-80) cc_final: 0.8013 (m-80) REVERT: S 83 MET cc_start: 0.8889 (mtm) cc_final: 0.8687 (mtp) outliers start: 1 outliers final: 1 residues processed: 176 average time/residue: 1.2776 time to fit residues: 239.9778 Evaluate side-chains 133 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 75 GLN G 18 GLN R 61 GLN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9817 Z= 0.191 Angle : 0.568 6.543 13290 Z= 0.304 Chirality : 0.042 0.164 1501 Planarity : 0.004 0.046 1667 Dihedral : 6.344 57.874 1377 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.48 % Allowed : 8.00 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.85 (0.24), residues: 1196 helix: 1.78 (0.25), residues: 411 sheet: 0.99 (0.30), residues: 269 loop : -0.67 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.023 0.002 PHE R 32 TYR 0.019 0.002 TYR S 103 ARG 0.008 0.001 ARG R 318 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.7975 (tptp) cc_final: 0.7385 (mmpt) REVERT: B 101 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7806 (mpp) outliers start: 26 outliers final: 12 residues processed: 149 average time/residue: 1.3013 time to fit residues: 207.1081 Evaluate side-chains 141 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.0270 chunk 33 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9817 Z= 0.140 Angle : 0.492 6.305 13290 Z= 0.266 Chirality : 0.041 0.152 1501 Planarity : 0.004 0.052 1667 Dihedral : 5.612 49.776 1377 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.81 % Allowed : 10.86 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1196 helix: 2.23 (0.25), residues: 410 sheet: 1.07 (0.31), residues: 269 loop : -0.55 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS L 27 PHE 0.020 0.001 PHE R 32 TYR 0.016 0.001 TYR S 190 ARG 0.009 0.001 ARG R 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 76 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7699 (mtpt) outliers start: 19 outliers final: 6 residues processed: 146 average time/residue: 1.3482 time to fit residues: 210.4270 Evaluate side-chains 136 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 0.0770 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 75 GLN B 266 HIS S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9817 Z= 0.187 Angle : 0.521 6.734 13290 Z= 0.280 Chirality : 0.042 0.170 1501 Planarity : 0.004 0.060 1667 Dihedral : 5.594 58.853 1377 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.57 % Allowed : 12.57 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.24), residues: 1196 helix: 2.38 (0.25), residues: 414 sheet: 0.84 (0.30), residues: 278 loop : -0.46 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.001 PHE R 45 TYR 0.020 0.001 TYR S 190 ARG 0.009 0.001 ARG R 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7872 (pmm) cc_final: 0.7513 (pp-130) REVERT: G 58 GLU cc_start: 0.7188 (pt0) cc_final: 0.6780 (pt0) REVERT: R 174 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8107 (p) REVERT: S 76 LYS cc_start: 0.7921 (mtpp) cc_final: 0.7678 (mtpt) outliers start: 27 outliers final: 15 residues processed: 136 average time/residue: 1.3868 time to fit residues: 200.7812 Evaluate side-chains 143 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9817 Z= 0.201 Angle : 0.520 7.301 13290 Z= 0.281 Chirality : 0.042 0.167 1501 Planarity : 0.004 0.058 1667 Dihedral : 5.352 43.547 1377 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.48 % Allowed : 12.48 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.24), residues: 1196 helix: 2.40 (0.25), residues: 416 sheet: 0.82 (0.31), residues: 272 loop : -0.51 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.002 PHE R 45 TYR 0.020 0.001 TYR S 190 ARG 0.009 0.000 ARG R 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8387 (tmmt) cc_final: 0.8028 (mmmm) REVERT: B 23 LYS cc_start: 0.8040 (tptp) cc_final: 0.7490 (tmmt) REVERT: B 217 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7484 (pp-130) REVERT: G 58 GLU cc_start: 0.7094 (pt0) cc_final: 0.6762 (pt0) REVERT: R 174 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8234 (p) REVERT: R 206 PHE cc_start: 0.7930 (m-10) cc_final: 0.7697 (m-80) REVERT: S 76 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7672 (mtpt) outliers start: 26 outliers final: 16 residues processed: 139 average time/residue: 1.3577 time to fit residues: 201.0591 Evaluate side-chains 146 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 239 ASN B 259 GLN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9817 Z= 0.151 Angle : 0.479 6.465 13290 Z= 0.259 Chirality : 0.040 0.158 1501 Planarity : 0.004 0.059 1667 Dihedral : 5.077 45.642 1377 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.95 % Allowed : 12.95 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.24), residues: 1196 helix: 2.51 (0.25), residues: 415 sheet: 0.80 (0.31), residues: 277 loop : -0.44 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.001 PHE R 45 TYR 0.017 0.001 TYR S 190 ARG 0.010 0.000 ARG R 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8475 (tmmt) cc_final: 0.8067 (mmmt) REVERT: B 217 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7441 (pp-130) REVERT: G 58 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6725 (pt0) REVERT: G 62 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6412 (ptp-170) REVERT: R 166 MET cc_start: 0.6471 (mmt) cc_final: 0.6257 (mmp) REVERT: R 174 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8144 (p) REVERT: R 206 PHE cc_start: 0.7927 (m-10) cc_final: 0.7705 (m-80) outliers start: 31 outliers final: 19 residues processed: 143 average time/residue: 1.2996 time to fit residues: 198.5622 Evaluate side-chains 152 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 259 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9817 Z= 0.167 Angle : 0.495 6.715 13290 Z= 0.267 Chirality : 0.041 0.166 1501 Planarity : 0.004 0.059 1667 Dihedral : 5.136 48.144 1377 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.86 % Allowed : 12.95 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1196 helix: 2.44 (0.25), residues: 417 sheet: 0.80 (0.31), residues: 277 loop : -0.42 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE R 45 TYR 0.019 0.001 TYR S 190 ARG 0.012 0.000 ARG R 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8475 (tmmt) cc_final: 0.8073 (mmmt) REVERT: B 217 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7476 (pp-130) REVERT: G 58 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6742 (pt0) REVERT: R 174 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8162 (p) REVERT: R 206 PHE cc_start: 0.7919 (m-10) cc_final: 0.7706 (m-80) outliers start: 30 outliers final: 19 residues processed: 137 average time/residue: 1.3608 time to fit residues: 198.6689 Evaluate side-chains 146 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9817 Z= 0.211 Angle : 0.529 8.864 13290 Z= 0.284 Chirality : 0.042 0.173 1501 Planarity : 0.004 0.057 1667 Dihedral : 5.406 58.008 1377 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.24 % Allowed : 13.05 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.24), residues: 1196 helix: 2.45 (0.25), residues: 415 sheet: 0.80 (0.30), residues: 276 loop : -0.50 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.002 PHE R 45 TYR 0.022 0.001 TYR S 190 ARG 0.012 0.001 ARG R 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7708 (mtt90) cc_final: 0.7484 (mmt90) REVERT: A 51 LYS cc_start: 0.8505 (tmmt) cc_final: 0.8101 (mmmt) REVERT: G 58 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6787 (pt0) REVERT: R 206 PHE cc_start: 0.7934 (m-10) cc_final: 0.7716 (m-80) outliers start: 34 outliers final: 23 residues processed: 137 average time/residue: 1.3888 time to fit residues: 202.8865 Evaluate side-chains 147 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9817 Z= 0.179 Angle : 0.511 8.559 13290 Z= 0.272 Chirality : 0.041 0.166 1501 Planarity : 0.004 0.058 1667 Dihedral : 5.312 54.177 1377 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.76 % Allowed : 14.19 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.24), residues: 1196 helix: 2.51 (0.25), residues: 415 sheet: 0.83 (0.30), residues: 276 loop : -0.47 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE R 45 TYR 0.019 0.001 TYR S 190 ARG 0.013 0.001 ARG R 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7684 (mtt90) cc_final: 0.7451 (mmt90) REVERT: A 51 LYS cc_start: 0.8504 (tmmt) cc_final: 0.8097 (mmmt) REVERT: G 58 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6775 (pt0) REVERT: R 206 PHE cc_start: 0.7929 (m-10) cc_final: 0.7713 (m-80) outliers start: 29 outliers final: 22 residues processed: 136 average time/residue: 1.2859 time to fit residues: 186.6712 Evaluate side-chains 146 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 117 optimal weight: 0.0570 chunk 108 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9817 Z= 0.148 Angle : 0.487 9.173 13290 Z= 0.259 Chirality : 0.040 0.160 1501 Planarity : 0.004 0.058 1667 Dihedral : 5.111 50.449 1377 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 14.76 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1196 helix: 2.58 (0.25), residues: 415 sheet: 0.87 (0.30), residues: 279 loop : -0.46 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE R 45 TYR 0.018 0.001 TYR S 190 ARG 0.013 0.000 ARG R 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8488 (tmmt) cc_final: 0.8088 (mmmt) REVERT: R 174 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8194 (p) outliers start: 24 outliers final: 19 residues processed: 132 average time/residue: 1.3322 time to fit residues: 187.7114 Evaluate side-chains 139 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.198221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139106 restraints weight = 9906.448| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.97 r_work: 0.3384 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9817 Z= 0.164 Angle : 0.499 9.871 13290 Z= 0.265 Chirality : 0.040 0.164 1501 Planarity : 0.004 0.058 1667 Dihedral : 5.051 48.109 1377 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.19 % Allowed : 15.33 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.24), residues: 1196 helix: 2.58 (0.25), residues: 415 sheet: 0.86 (0.30), residues: 280 loop : -0.44 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.001 PHE R 45 TYR 0.019 0.001 TYR S 190 ARG 0.013 0.000 ARG R 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4100.32 seconds wall clock time: 73 minutes 45.27 seconds (4425.27 seconds total)