Starting phenix.real_space_refine on Sat Feb 17 09:37:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w55_32314/02_2024/7w55_32314.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w55_32314/02_2024/7w55_32314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w55_32314/02_2024/7w55_32314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w55_32314/02_2024/7w55_32314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w55_32314/02_2024/7w55_32314.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w55_32314/02_2024/7w55_32314.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 5889 2.51 5 N 1580 2.21 5 O 1698 1.98 5 H 9112 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 250": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 165": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 18334 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3799 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5108 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 157 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3493 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 827 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 4950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4950 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain breaks: 1 Time building chain proxies: 7.87, per 1000 atoms: 0.43 Number of scatterers: 18334 At special positions: 0 Unit cell: (115.56, 129.6, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 O 1698 8.00 N 1580 7.00 C 5889 6.00 H 9112 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 204 " distance=2.06 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: 14.17 Conformation dependent library (CDL) restraints added in 1.8 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 14 sheets defined 42.1% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.720A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.534A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.360A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.282A pdb=" N THR A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.888A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.754A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 54 through 58 removed outlier: 3.750A pdb=" N ASN G 58 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 73 removed outlier: 3.608A pdb=" N VAL R 51 " --> pdb=" O PRO R 47 " (cutoff:3.500A) Proline residue: R 54 - end of helix removed outlier: 3.717A pdb=" N LEU R 71 " --> pdb=" O CYS R 67 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 77 Processing helix chain 'R' and resid 78 through 108 Proline residue: R 100 - end of helix Processing helix chain 'R' and resid 115 through 150 Processing helix chain 'R' and resid 150 through 158 Processing helix chain 'R' and resid 159 through 184 Proline residue: R 180 - end of helix removed outlier: 3.859A pdb=" N ILE R 184 " --> pdb=" O PRO R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 225 removed outlier: 3.616A pdb=" N TYR R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 245 Processing helix chain 'R' and resid 246 through 250 Processing helix chain 'R' and resid 258 through 294 removed outlier: 4.310A pdb=" N CYS R 262 " --> pdb=" O ILE R 258 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER R 265 " --> pdb=" O PRO R 261 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS R 268 " --> pdb=" O LYS R 264 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.539A pdb=" N VAL R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 328 removed outlier: 3.565A pdb=" N SER R 320 " --> pdb=" O PHE R 316 " (cutoff:3.500A) Proline residue: R 324 - end of helix Processing helix chain 'R' and resid 331 through 346 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 9.467A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.894A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.618A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.790A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 158 removed outlier: 3.602A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N CYS B 171 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.583A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.528A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.803A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.991A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 4.376A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.316A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 185 through 187 495 hydrogen bonds defined for protein. 1365 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: 6.47 Time building geometry restraints manager: 14.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9083 1.02 - 1.21: 43 1.21 - 1.41: 3934 1.41 - 1.61: 5398 1.61 - 1.81: 81 Bond restraints: 18539 Sorted by residual: bond pdb=" SG CYS R 204 " pdb=" HG CYS R 204 " ideal model delta sigma weight residual 1.200 1.344 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" SG CYS R 67 " pdb=" HG CYS R 67 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" CA GLU E 234 " pdb=" C GLU E 234 " ideal model delta sigma weight residual 1.523 1.439 0.084 1.21e-02 6.83e+03 4.81e+01 bond pdb=" SG CYS R 119 " pdb=" HG CYS R 119 " ideal model delta sigma weight residual 1.200 1.332 -0.132 2.00e-02 2.50e+03 4.32e+01 bond pdb=" CA ALA B 145 " pdb=" C ALA B 145 " ideal model delta sigma weight residual 1.521 1.462 0.059 1.24e-02 6.50e+03 2.26e+01 ... (remaining 18534 not shown) Histogram of bond angle deviations from ideal: 94.09 - 102.45: 37 102.45 - 110.80: 19193 110.80 - 119.16: 5835 119.16 - 127.52: 8172 127.52 - 135.88: 101 Bond angle restraints: 33338 Sorted by residual: angle pdb=" N LEU R 113 " pdb=" CA LEU R 113 " pdb=" C LEU R 113 " ideal model delta sigma weight residual 111.40 127.18 -15.78 1.22e+00 6.72e-01 1.67e+02 angle pdb=" N PHE R 114 " pdb=" CA PHE R 114 " pdb=" C PHE R 114 " ideal model delta sigma weight residual 111.36 124.83 -13.47 1.09e+00 8.42e-01 1.53e+02 angle pdb=" N HIS R 190 " pdb=" CA HIS R 190 " pdb=" C HIS R 190 " ideal model delta sigma weight residual 110.44 99.99 10.45 1.20e+00 6.94e-01 7.59e+01 angle pdb=" N GLU B 231 " pdb=" CA GLU B 231 " pdb=" C GLU B 231 " ideal model delta sigma weight residual 110.44 100.62 9.82 1.20e+00 6.94e-01 6.69e+01 angle pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" C TYR E 235 " ideal model delta sigma weight residual 109.81 126.35 -16.54 2.21e+00 2.05e-01 5.60e+01 ... (remaining 33333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8110 17.79 - 35.58: 410 35.58 - 53.36: 160 53.36 - 71.15: 79 71.15 - 88.94: 12 Dihedral angle restraints: 8771 sinusoidal: 4676 harmonic: 4095 Sorted by residual: dihedral pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " ideal model delta harmonic sigma weight residual 122.80 145.40 -22.60 0 2.50e+00 1.60e-01 8.17e+01 dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 204 " pdb=" CB CYS R 204 " ideal model delta sinusoidal sigma weight residual 93.00 168.64 -75.64 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" C TYR E 235 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " ideal model delta harmonic sigma weight residual -122.60 -143.60 21.00 0 2.50e+00 1.60e-01 7.05e+01 ... (remaining 8768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 1427 0.230 - 0.460: 4 0.460 - 0.689: 2 0.689 - 0.919: 0 0.919 - 1.149: 1 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.30e+01 chirality pdb=" CA PHE R 114 " pdb=" N PHE R 114 " pdb=" C PHE R 114 " pdb=" CB PHE R 114 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CA TYR B 64 " pdb=" N TYR B 64 " pdb=" C TYR B 64 " pdb=" CB TYR B 64 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.42e+00 ... (remaining 1431 not shown) Planarity restraints: 2740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 204 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C CYS R 204 " 0.058 2.00e-02 2.50e+03 pdb=" O CYS R 204 " -0.021 2.00e-02 2.50e+03 pdb=" N THR R 205 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 145 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" N GLY B 146 " 0.048 2.00e-02 2.50e+03 pdb=" CA GLY B 146 " -0.013 2.00e-02 2.50e+03 pdb=" H GLY B 146 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 145 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C ALA B 145 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA B 145 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 146 " -0.016 2.00e-02 2.50e+03 ... (remaining 2737 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 695 2.16 - 2.77: 35930 2.77 - 3.38: 52764 3.38 - 3.99: 68568 3.99 - 4.60: 107025 Nonbonded interactions: 264982 Sorted by model distance: nonbonded pdb=" HG1 THR B 279 " pdb=" O VAL B 320 " model vdw 1.551 1.850 nonbonded pdb="HH12 ARG A 208 " pdb=" OD1 ASP A 239 " model vdw 1.580 1.850 nonbonded pdb="HH11 ARG C 24 " pdb=" OE2 GLU R 102 " model vdw 1.605 1.850 nonbonded pdb=" OD2 ASP B 175 " pdb=" HG1 THR B 178 " model vdw 1.635 1.850 nonbonded pdb=" HG SER B 250 " pdb=" OD1 ASP B 252 " model vdw 1.637 1.850 ... (remaining 264977 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=0.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.250 Extract box with map and model: 2.680 Check model and map are aligned: 0.310 Set scattering table: 0.210 Process input model: 56.640 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 9427 Z= 0.333 Angle : 0.721 16.538 12773 Z= 0.454 Chirality : 0.058 1.149 1434 Planarity : 0.004 0.033 1622 Dihedral : 11.825 88.940 3392 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.50 % Allowed : 4.95 % Favored : 94.55 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1148 helix: 1.24 (0.24), residues: 420 sheet: 0.28 (0.32), residues: 278 loop : -0.12 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 211 HIS 0.009 0.001 HIS B 147 PHE 0.019 0.001 PHE R 284 TYR 0.021 0.002 TYR E 235 ARG 0.003 0.000 ARG R 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 317 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 312 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASN cc_start: 0.7524 (p0) cc_final: 0.6887 (p0) REVERT: A 229 ASP cc_start: 0.7118 (t0) cc_final: 0.6639 (t0) REVERT: A 230 TYR cc_start: 0.8340 (m-10) cc_final: 0.8086 (m-10) REVERT: A 231 ASN cc_start: 0.8050 (m-40) cc_final: 0.7646 (m-40) REVERT: A 232 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7828 (mmm-85) REVERT: A 263 LEU cc_start: 0.8201 (mt) cc_final: 0.7983 (mt) REVERT: A 284 ARG cc_start: 0.7526 (ptp-170) cc_final: 0.7319 (ptp-110) REVERT: A 311 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 348 ASP cc_start: 0.7408 (t70) cc_final: 0.7188 (t70) REVERT: B 42 ILE cc_start: 0.8677 (tt) cc_final: 0.8464 (tt) REVERT: B 141 SER cc_start: 0.7973 (t) cc_final: 0.7706 (p) REVERT: B 273 ASN cc_start: 0.6809 (m110) cc_final: 0.6526 (m110) REVERT: C 24 ARG cc_start: 0.7639 (ttm-80) cc_final: 0.7303 (ttm-80) REVERT: E 66 ARG cc_start: 0.7736 (mtm-85) cc_final: 0.7307 (mtm-85) REVERT: E 82 MET cc_start: 0.7794 (mtt) cc_final: 0.7578 (mtp) REVERT: E 214 LEU cc_start: 0.8312 (tp) cc_final: 0.8083 (tp) REVERT: G 18 LEU cc_start: 0.7934 (mm) cc_final: 0.7552 (mt) REVERT: G 29 VAL cc_start: 0.8890 (t) cc_final: 0.8569 (t) REVERT: R 49 SER cc_start: 0.7652 (t) cc_final: 0.7451 (m) REVERT: R 76 MET cc_start: 0.6543 (tpt) cc_final: 0.6334 (mmm) REVERT: R 204 CYS cc_start: 0.5915 (t) cc_final: 0.5552 (t) REVERT: R 242 ARG cc_start: 0.7319 (tpp80) cc_final: 0.6904 (tpt170) REVERT: R 291 PHE cc_start: 0.7918 (t80) cc_final: 0.7672 (t80) REVERT: R 320 SER cc_start: 0.8363 (m) cc_final: 0.8100 (t) outliers start: 5 outliers final: 1 residues processed: 316 average time/residue: 2.2612 time to fit residues: 769.3963 Evaluate side-chains 271 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 190 GLN B 41 ASN B 80 GLN B 180 GLN R 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9427 Z= 0.292 Angle : 0.570 6.925 12773 Z= 0.310 Chirality : 0.042 0.222 1434 Planarity : 0.004 0.037 1622 Dihedral : 5.534 40.233 1273 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.28 % Allowed : 15.84 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1148 helix: 1.43 (0.25), residues: 427 sheet: -0.09 (0.31), residues: 270 loop : -0.17 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 87 HIS 0.007 0.001 HIS R 185 PHE 0.019 0.002 PHE R 284 TYR 0.027 0.002 TYR E 235 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 265 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.8076 (m-40) cc_final: 0.7847 (m-40) REVERT: A 314 ASP cc_start: 0.7089 (t70) cc_final: 0.6826 (t70) REVERT: B 42 ILE cc_start: 0.8700 (tt) cc_final: 0.8456 (tt) REVERT: B 224 ARG cc_start: 0.7125 (mtp180) cc_final: 0.6876 (ttm110) REVERT: B 273 ASN cc_start: 0.6794 (m110) cc_final: 0.6516 (m110) REVERT: B 282 SER cc_start: 0.8188 (t) cc_final: 0.7986 (m) REVERT: C 24 ARG cc_start: 0.7639 (ttm-80) cc_final: 0.7275 (ttm-80) REVERT: E 18 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8320 (ttmm) REVERT: E 210 THR cc_start: 0.8349 (t) cc_final: 0.8104 (m) REVERT: E 214 LEU cc_start: 0.8392 (tp) cc_final: 0.8184 (tp) REVERT: G 18 LEU cc_start: 0.7953 (mm) cc_final: 0.7618 (mt) REVERT: G 29 VAL cc_start: 0.8905 (t) cc_final: 0.8667 (t) REVERT: R 320 SER cc_start: 0.8395 (m) cc_final: 0.8146 (t) outliers start: 23 outliers final: 14 residues processed: 274 average time/residue: 2.2883 time to fit residues: 675.4445 Evaluate side-chains 266 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 252 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9427 Z= 0.387 Angle : 0.579 7.408 12773 Z= 0.316 Chirality : 0.043 0.250 1434 Planarity : 0.004 0.040 1622 Dihedral : 5.314 27.121 1271 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.37 % Allowed : 16.73 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1148 helix: 1.45 (0.25), residues: 428 sheet: -0.36 (0.30), residues: 268 loop : -0.25 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 174 HIS 0.006 0.002 HIS R 185 PHE 0.022 0.002 PHE R 284 TYR 0.029 0.002 TYR E 235 ARG 0.005 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 256 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7477 (ttm-80) cc_final: 0.7269 (ttm-80) REVERT: A 214 CYS cc_start: 0.7655 (m) cc_final: 0.7452 (m) REVERT: A 231 ASN cc_start: 0.8160 (m-40) cc_final: 0.7892 (m-40) REVERT: B 42 ILE cc_start: 0.8697 (tt) cc_final: 0.8479 (tt) REVERT: B 53 ARG cc_start: 0.7992 (mmt180) cc_final: 0.7751 (mmt-90) REVERT: B 263 ASP cc_start: 0.7157 (t0) cc_final: 0.6920 (t70) REVERT: B 273 ASN cc_start: 0.6816 (m110) cc_final: 0.6538 (m110) REVERT: B 282 SER cc_start: 0.8229 (t) cc_final: 0.7997 (m) REVERT: C 24 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.7368 (ttm-80) REVERT: E 18 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8332 (ttmm) REVERT: E 210 THR cc_start: 0.8375 (t) cc_final: 0.8174 (m) REVERT: G 29 VAL cc_start: 0.8901 (t) cc_final: 0.8633 (t) outliers start: 34 outliers final: 22 residues processed: 272 average time/residue: 2.3799 time to fit residues: 697.7438 Evaluate side-chains 278 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 256 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 311 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 180 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 9427 Z= 0.459 Angle : 0.595 6.720 12773 Z= 0.322 Chirality : 0.044 0.245 1434 Planarity : 0.005 0.043 1622 Dihedral : 5.285 25.553 1271 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.06 % Allowed : 16.73 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1148 helix: 1.38 (0.25), residues: 428 sheet: -0.58 (0.30), residues: 266 loop : -0.42 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 174 HIS 0.007 0.002 HIS R 43 PHE 0.025 0.002 PHE R 284 TYR 0.026 0.002 TYR E 235 ARG 0.005 0.001 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 258 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ILE cc_start: 0.8733 (tt) cc_final: 0.8521 (tt) REVERT: B 263 ASP cc_start: 0.7238 (t0) cc_final: 0.7000 (t70) REVERT: B 273 ASN cc_start: 0.6823 (m110) cc_final: 0.6566 (m110) REVERT: B 282 SER cc_start: 0.8218 (t) cc_final: 0.7982 (m) REVERT: B 339 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7604 (p) REVERT: C 24 ARG cc_start: 0.7762 (ttm-80) cc_final: 0.7364 (ttm-80) REVERT: E 18 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8345 (ttmm) REVERT: G 29 VAL cc_start: 0.8890 (t) cc_final: 0.8611 (t) REVERT: R 77 LYS cc_start: 0.7953 (tttt) cc_final: 0.7737 (tttt) outliers start: 41 outliers final: 27 residues processed: 276 average time/residue: 2.2831 time to fit residues: 678.9080 Evaluate side-chains 279 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 251 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 311 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9427 Z= 0.225 Angle : 0.533 5.792 12773 Z= 0.285 Chirality : 0.040 0.191 1434 Planarity : 0.004 0.042 1622 Dihedral : 4.960 25.385 1271 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.27 % Allowed : 18.61 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1148 helix: 1.81 (0.25), residues: 422 sheet: -0.57 (0.29), residues: 270 loop : -0.27 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 174 HIS 0.008 0.001 HIS R 43 PHE 0.020 0.002 PHE R 224 TYR 0.022 0.001 TYR E 235 ARG 0.003 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 258 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7165 (mtp-110) REVERT: B 41 ASN cc_start: 0.7790 (m-40) cc_final: 0.7577 (m110) REVERT: B 42 ILE cc_start: 0.8714 (tt) cc_final: 0.8506 (tt) REVERT: B 73 ARG cc_start: 0.7878 (ttt180) cc_final: 0.7586 (ttt180) REVERT: B 195 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7192 (mp) REVERT: B 256 ARG cc_start: 0.8350 (mtt90) cc_final: 0.8128 (mtt90) REVERT: B 263 ASP cc_start: 0.7259 (t0) cc_final: 0.6966 (t70) REVERT: B 273 ASN cc_start: 0.6822 (m110) cc_final: 0.6555 (m110) REVERT: B 282 SER cc_start: 0.8230 (t) cc_final: 0.8025 (m) REVERT: B 339 SER cc_start: 0.7909 (OUTLIER) cc_final: 0.7570 (p) REVERT: C 24 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7223 (ttm-80) REVERT: E 18 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8328 (ttmm) REVERT: E 22 SER cc_start: 0.8055 (m) cc_final: 0.7722 (p) REVERT: G 18 LEU cc_start: 0.7948 (mm) cc_final: 0.7639 (mt) REVERT: G 29 VAL cc_start: 0.8874 (t) cc_final: 0.8595 (t) outliers start: 33 outliers final: 22 residues processed: 269 average time/residue: 2.4417 time to fit residues: 703.9999 Evaluate side-chains 275 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 250 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 311 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9427 Z= 0.300 Angle : 0.539 5.622 12773 Z= 0.289 Chirality : 0.041 0.189 1434 Planarity : 0.004 0.044 1622 Dihedral : 4.886 24.542 1271 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.56 % Allowed : 18.91 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1148 helix: 1.85 (0.25), residues: 422 sheet: -0.55 (0.30), residues: 265 loop : -0.29 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 174 HIS 0.008 0.001 HIS R 43 PHE 0.021 0.002 PHE R 284 TYR 0.020 0.002 TYR E 235 ARG 0.006 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 250 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7158 (mtp-110) REVERT: B 42 ILE cc_start: 0.8734 (tt) cc_final: 0.8529 (tt) REVERT: B 73 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7586 (ttt180) REVERT: B 195 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7222 (mp) REVERT: B 273 ASN cc_start: 0.6825 (m110) cc_final: 0.6559 (m110) REVERT: B 282 SER cc_start: 0.8230 (t) cc_final: 0.7999 (m) REVERT: B 339 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7601 (p) REVERT: E 22 SER cc_start: 0.8069 (OUTLIER) cc_final: 0.7738 (p) REVERT: G 18 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7671 (mt) REVERT: G 29 VAL cc_start: 0.8878 (t) cc_final: 0.8592 (t) outliers start: 36 outliers final: 23 residues processed: 262 average time/residue: 2.3115 time to fit residues: 651.6472 Evaluate side-chains 278 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 250 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 311 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 41 ASN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9427 Z= 0.224 Angle : 0.519 5.357 12773 Z= 0.277 Chirality : 0.040 0.168 1434 Planarity : 0.004 0.046 1622 Dihedral : 4.753 23.772 1271 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.17 % Allowed : 19.50 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1148 helix: 2.05 (0.25), residues: 421 sheet: -0.57 (0.30), residues: 265 loop : -0.25 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 297 HIS 0.009 0.001 HIS R 43 PHE 0.018 0.001 PHE R 284 TYR 0.019 0.001 TYR E 235 ARG 0.006 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 252 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7151 (mtp-110) REVERT: B 41 ASN cc_start: 0.7854 (m-40) cc_final: 0.7649 (m110) REVERT: B 73 ARG cc_start: 0.7808 (ttt180) cc_final: 0.7528 (ttt90) REVERT: B 195 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7158 (mp) REVERT: B 273 ASN cc_start: 0.6820 (m110) cc_final: 0.6530 (m110) REVERT: B 282 SER cc_start: 0.8229 (t) cc_final: 0.8022 (m) REVERT: B 339 SER cc_start: 0.7920 (OUTLIER) cc_final: 0.7607 (p) REVERT: C 24 ARG cc_start: 0.7682 (ttm-80) cc_final: 0.7221 (ttm-80) REVERT: G 18 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7667 (mt) REVERT: G 29 VAL cc_start: 0.8860 (t) cc_final: 0.8578 (t) outliers start: 32 outliers final: 22 residues processed: 264 average time/residue: 2.4132 time to fit residues: 686.5396 Evaluate side-chains 272 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 246 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 311 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 50.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 245 ASN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 9427 Z= 0.472 Angle : 0.588 6.229 12773 Z= 0.318 Chirality : 0.044 0.211 1434 Planarity : 0.005 0.045 1622 Dihedral : 4.982 23.900 1271 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.37 % Allowed : 19.60 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1148 helix: 1.76 (0.25), residues: 422 sheet: -0.66 (0.30), residues: 268 loop : -0.39 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 104 HIS 0.009 0.002 HIS R 43 PHE 0.027 0.002 PHE R 284 TYR 0.026 0.002 TYR E 235 ARG 0.008 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 250 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7150 (mtp-110) REVERT: B 73 ARG cc_start: 0.7901 (ttt180) cc_final: 0.7647 (ttt180) REVERT: B 195 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7271 (mp) REVERT: B 273 ASN cc_start: 0.6827 (m110) cc_final: 0.6550 (m110) REVERT: B 282 SER cc_start: 0.8237 (t) cc_final: 0.7991 (m) REVERT: B 339 SER cc_start: 0.7944 (OUTLIER) cc_final: 0.7640 (p) REVERT: C 24 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7519 (ttm-80) REVERT: E 22 SER cc_start: 0.8096 (m) cc_final: 0.7742 (p) REVERT: G 29 VAL cc_start: 0.8875 (t) cc_final: 0.8612 (t) REVERT: R 192 PHE cc_start: 0.2449 (OUTLIER) cc_final: 0.1755 (p90) outliers start: 34 outliers final: 26 residues processed: 263 average time/residue: 2.4677 time to fit residues: 695.5783 Evaluate side-chains 273 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 243 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 192 PHE Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 311 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 41 ASN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9427 Z= 0.226 Angle : 0.534 5.528 12773 Z= 0.285 Chirality : 0.040 0.174 1434 Planarity : 0.006 0.105 1622 Dihedral : 4.833 23.366 1271 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.57 % Allowed : 20.99 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1148 helix: 2.01 (0.25), residues: 419 sheet: -0.63 (0.30), residues: 265 loop : -0.35 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 174 HIS 0.010 0.001 HIS R 43 PHE 0.019 0.002 PHE R 284 TYR 0.019 0.001 TYR E 235 ARG 0.018 0.001 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 252 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7137 (mtp-110) REVERT: B 142 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7437 (mmt-90) REVERT: B 195 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7144 (mp) REVERT: B 273 ASN cc_start: 0.6815 (m110) cc_final: 0.6536 (m110) REVERT: B 282 SER cc_start: 0.8236 (t) cc_final: 0.8019 (m) REVERT: B 339 SER cc_start: 0.7941 (OUTLIER) cc_final: 0.7623 (p) REVERT: E 22 SER cc_start: 0.8063 (m) cc_final: 0.7748 (p) REVERT: G 29 VAL cc_start: 0.8855 (t) cc_final: 0.8596 (t) REVERT: R 192 PHE cc_start: 0.2286 (OUTLIER) cc_final: 0.1687 (p90) outliers start: 26 outliers final: 18 residues processed: 261 average time/residue: 2.3355 time to fit residues: 655.8097 Evaluate side-chains 274 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 251 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 192 PHE Chi-restraints excluded: chain R residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 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 245 ASN B 41 ASN B 80 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9427 Z= 0.291 Angle : 0.556 7.856 12773 Z= 0.295 Chirality : 0.041 0.175 1434 Planarity : 0.006 0.099 1622 Dihedral : 4.827 22.778 1271 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.57 % Allowed : 21.39 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1148 helix: 1.98 (0.25), residues: 419 sheet: -0.64 (0.31), residues: 260 loop : -0.39 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 174 HIS 0.010 0.001 HIS R 43 PHE 0.020 0.002 PHE R 284 TYR 0.020 0.001 TYR E 235 ARG 0.019 0.001 ARG B 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 258 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7132 (mtp-110) REVERT: B 142 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7460 (mmt-90) REVERT: B 195 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7184 (mp) REVERT: B 273 ASN cc_start: 0.6818 (m110) cc_final: 0.6539 (m110) REVERT: B 282 SER cc_start: 0.8227 (t) cc_final: 0.8021 (m) REVERT: B 339 SER cc_start: 0.7929 (OUTLIER) cc_final: 0.7626 (p) REVERT: E 22 SER cc_start: 0.8070 (m) cc_final: 0.7754 (p) REVERT: G 29 VAL cc_start: 0.8885 (t) cc_final: 0.8628 (t) REVERT: R 192 PHE cc_start: 0.2243 (OUTLIER) cc_final: 0.1598 (p90) outliers start: 26 outliers final: 17 residues processed: 267 average time/residue: 2.4833 time to fit residues: 710.0131 Evaluate side-chains 276 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 254 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 192 PHE Chi-restraints excluded: chain R residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 80 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120507 restraints weight = 36718.657| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.94 r_work: 0.3489 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9427 Z= 0.205 Angle : 0.530 5.848 12773 Z= 0.280 Chirality : 0.040 0.157 1434 Planarity : 0.006 0.095 1622 Dihedral : 4.669 22.108 1271 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.18 % Allowed : 22.28 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1148 helix: 2.10 (0.25), residues: 424 sheet: -0.58 (0.31), residues: 259 loop : -0.29 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 174 HIS 0.011 0.001 HIS R 43 PHE 0.018 0.001 PHE R 284 TYR 0.017 0.001 TYR E 235 ARG 0.018 0.001 ARG B 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10428.66 seconds wall clock time: 182 minutes 38.77 seconds (10958.77 seconds total)