Starting phenix.real_space_refine on Thu Mar 14 22:02:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rg9_24445/03_2024/7rg9_24445_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rg9_24445/03_2024/7rg9_24445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rg9_24445/03_2024/7rg9_24445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rg9_24445/03_2024/7rg9_24445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rg9_24445/03_2024/7rg9_24445_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rg9_24445/03_2024/7rg9_24445_neut.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6223 2.51 5 N 1677 2.21 5 O 1811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "R ARG 227": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 326": "NH1" <-> "NH2" Residue "R ARG 348": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R GLU 412": "OE1" <-> "OE2" Residue "R ARG 414": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9769 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1792 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2193 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 5.43, per 1000 atoms: 0.56 Number of scatterers: 9769 At special positions: 0 Unit cell: (129.792, 108.992, 104, 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 58 16.00 O 1811 8.00 N 1677 7.00 C 6223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 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: 3.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 35.2% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.584A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.415A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.697A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.537A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.200A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 4.098A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.811A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.749A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.539A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.722A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 169 removed outlier: 3.616A pdb=" N LEU R 144 " --> pdb=" O GLN R 140 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 197 removed outlier: 3.734A pdb=" N HIS R 180 " --> pdb=" O ARG R 176 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG R 190 " --> pdb=" O SER R 186 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU R 192 " --> pdb=" O ILE R 188 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 202 removed outlier: 3.677A pdb=" N LEU R 201 " --> pdb=" O LYS R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 207 Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 223 through 257 removed outlier: 3.918A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU R 245 " --> pdb=" O TYR R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 291 removed outlier: 4.375A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 306 through 338 removed outlier: 3.990A pdb=" N ARG R 310 " --> pdb=" O TRP R 306 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 367 removed outlier: 3.595A pdb=" N PHE R 367 " --> pdb=" O GLU R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 403 removed outlier: 3.748A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA R 399 " --> pdb=" O GLY R 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 419 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 5.978A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.505A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.674A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.136A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.666A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.632A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.947A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.326A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.983A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.983A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.796A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.910A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1290 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: 2.83 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1617 1.32 - 1.44: 2812 1.44 - 1.57: 5467 1.57 - 1.69: 0 1.69 - 1.82: 82 Bond restraints: 9978 Sorted by residual: bond pdb=" CA SER B 227 " pdb=" CB SER B 227 " ideal model delta sigma weight residual 1.531 1.478 0.053 1.48e-02 4.57e+03 1.27e+01 bond pdb=" N ARG N 105 " pdb=" CA ARG N 105 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.16e-02 7.43e+03 1.12e+01 bond pdb=" C ASP G 48 " pdb=" O ASP G 48 " ideal model delta sigma weight residual 1.238 1.197 0.041 1.28e-02 6.10e+03 1.04e+01 bond pdb=" N GLU B 226 " pdb=" CA GLU B 226 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.37e+00 bond pdb=" CA SER B 74 " pdb=" CB SER B 74 " ideal model delta sigma weight residual 1.532 1.482 0.050 1.74e-02 3.30e+03 8.36e+00 ... (remaining 9973 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 151 105.81 - 112.87: 5084 112.87 - 119.93: 3667 119.93 - 126.99: 4498 126.99 - 134.05: 122 Bond angle restraints: 13522 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.18 105.07 8.11 1.21e+00 6.83e-01 4.50e+01 angle pdb=" CA VAL B 187 " pdb=" C VAL B 187 " pdb=" O VAL B 187 " ideal model delta sigma weight residual 121.13 114.78 6.35 1.16e+00 7.43e-01 2.99e+01 angle pdb=" N ARG N 105 " pdb=" CA ARG N 105 " pdb=" C ARG N 105 " ideal model delta sigma weight residual 112.59 105.99 6.60 1.22e+00 6.72e-01 2.92e+01 angle pdb=" N ASP N 106 " pdb=" CA ASP N 106 " pdb=" CB ASP N 106 " ideal model delta sigma weight residual 110.63 102.35 8.28 1.63e+00 3.76e-01 2.58e+01 angle pdb=" CA ARG A 228 " pdb=" C ARG A 228 " pdb=" O ARG A 228 " ideal model delta sigma weight residual 121.87 116.41 5.46 1.16e+00 7.43e-01 2.21e+01 ... (remaining 13517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 5261 17.36 - 34.72: 496 34.72 - 52.08: 98 52.08 - 69.44: 16 69.44 - 86.80: 13 Dihedral angle restraints: 5884 sinusoidal: 2273 harmonic: 3611 Sorted by residual: dihedral pdb=" CA ASN G 59 " pdb=" C ASN G 59 " pdb=" N PRO G 60 " pdb=" CA PRO G 60 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 154.80 25.20 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA THR R 298 " pdb=" C THR R 298 " pdb=" N ARG R 299 " pdb=" CA ARG R 299 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 5881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1326 0.070 - 0.141: 172 0.141 - 0.211: 15 0.211 - 0.281: 4 0.281 - 0.352: 1 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CA PRO G 49 " pdb=" N PRO G 49 " pdb=" C PRO G 49 " pdb=" CB PRO G 49 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA HIS B 225 " pdb=" N HIS B 225 " pdb=" C HIS B 225 " pdb=" CB HIS B 225 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ASP B 76 " pdb=" N ASP B 76 " pdb=" C ASP B 76 " pdb=" CB ASP B 76 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1515 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 224 " -0.028 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C GLY B 224 " 0.094 2.00e-02 2.50e+03 pdb=" O GLY B 224 " -0.035 2.00e-02 2.50e+03 pdb=" N HIS B 225 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 111 " 0.021 2.00e-02 2.50e+03 2.91e-02 2.12e+01 pdb=" CG TRP E 111 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP E 111 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP E 111 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 111 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP E 111 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 111 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 111 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 111 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.020 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR B 59 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 101 2.51 - 3.11: 7711 3.11 - 3.71: 14840 3.71 - 4.30: 22394 4.30 - 4.90: 36626 Nonbonded interactions: 81672 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 1.916 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 1.995 2.440 nonbonded pdb=" NH1 ARG R 299 " pdb=" OD1 ASN R 300 " model vdw 2.027 2.520 nonbonded pdb=" OD1 ASN E 157 " pdb=" N GLY E 158 " model vdw 2.182 2.520 nonbonded pdb=" O LEU R 167 " pdb=" NE2 HIS R 173 " model vdw 2.213 2.520 ... (remaining 81667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 6.190 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.260 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 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 : 0.011 0.058 9978 Z= 0.745 Angle : 0.867 9.051 13522 Z= 0.516 Chirality : 0.051 0.352 1518 Planarity : 0.005 0.054 1712 Dihedral : 14.585 86.802 3543 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.76 % Allowed : 0.67 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.23), residues: 1218 helix: -0.74 (0.27), residues: 359 sheet: -1.60 (0.28), residues: 309 loop : -2.24 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP E 111 HIS 0.020 0.002 HIS A 357 PHE 0.021 0.002 PHE A 246 TYR 0.060 0.003 TYR B 59 ARG 0.013 0.001 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 205 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 TYR cc_start: 0.7146 (t80) cc_final: 0.6926 (t80) REVERT: G 42 GLU cc_start: 0.7429 (pp20) cc_final: 0.7045 (tm-30) REVERT: R 294 GLU cc_start: 0.6173 (mp0) cc_final: 0.5699 (mp0) REVERT: R 303 MET cc_start: 0.4455 (tpt) cc_final: 0.4054 (mmt) outliers start: 8 outliers final: 2 residues processed: 208 average time/residue: 0.2514 time to fit residues: 69.3681 Evaluate side-chains 167 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 220 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9978 Z= 0.223 Angle : 0.650 7.744 13522 Z= 0.343 Chirality : 0.044 0.178 1518 Planarity : 0.004 0.046 1712 Dihedral : 6.236 59.421 1366 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.62 % Allowed : 9.46 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.76 (0.24), residues: 1218 helix: -0.05 (0.27), residues: 372 sheet: -1.24 (0.28), residues: 313 loop : -1.87 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 243 HIS 0.013 0.001 HIS A 357 PHE 0.024 0.002 PHE R 280 TYR 0.011 0.002 TYR R 145 ARG 0.005 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 225 HIS cc_start: 0.6093 (OUTLIER) cc_final: 0.5761 (m-70) REVERT: G 42 GLU cc_start: 0.7606 (pp20) cc_final: 0.7323 (tm-30) REVERT: N 6 GLU cc_start: 0.5407 (OUTLIER) cc_final: 0.5162 (mp0) REVERT: R 170 ARG cc_start: 0.5127 (mmm160) cc_final: 0.4214 (mmt-90) REVERT: R 292 GLU cc_start: 0.7231 (mm-30) cc_final: 0.7021 (mm-30) REVERT: R 294 GLU cc_start: 0.6307 (mp0) cc_final: 0.6009 (mp0) outliers start: 17 outliers final: 11 residues processed: 204 average time/residue: 0.2441 time to fit residues: 66.8592 Evaluate side-chains 182 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 371 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 320 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9978 Z= 0.234 Angle : 0.625 7.617 13522 Z= 0.331 Chirality : 0.043 0.151 1518 Planarity : 0.004 0.050 1712 Dihedral : 5.954 56.064 1366 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.39 % Allowed : 13.09 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.24), residues: 1218 helix: 0.09 (0.27), residues: 378 sheet: -1.07 (0.28), residues: 315 loop : -1.65 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 243 HIS 0.010 0.001 HIS A 357 PHE 0.017 0.002 PHE R 280 TYR 0.021 0.002 TYR E 178 ARG 0.004 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.7116 (mpt-90) cc_final: 0.6916 (mtm-85) REVERT: B 225 HIS cc_start: 0.6294 (OUTLIER) cc_final: 0.5577 (m-70) REVERT: B 226 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.5924 (mt-10) REVERT: E 17 SER cc_start: 0.6843 (m) cc_final: 0.6638 (t) REVERT: G 42 GLU cc_start: 0.7655 (pp20) cc_final: 0.7419 (tm-30) REVERT: N 6 GLU cc_start: 0.5538 (OUTLIER) cc_final: 0.5315 (mp0) REVERT: R 170 ARG cc_start: 0.5170 (mmm160) cc_final: 0.4256 (mmt-90) REVERT: R 205 TYR cc_start: 0.3558 (OUTLIER) cc_final: 0.2523 (m-80) REVERT: R 294 GLU cc_start: 0.6275 (mp0) cc_final: 0.5952 (mp0) outliers start: 25 outliers final: 13 residues processed: 191 average time/residue: 0.2428 time to fit residues: 62.4459 Evaluate side-chains 176 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain R residue 205 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 0.0570 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 279 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 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 0.039 9978 Z= 0.288 Angle : 0.661 8.705 13522 Z= 0.348 Chirality : 0.044 0.152 1518 Planarity : 0.004 0.059 1712 Dihedral : 6.027 57.255 1366 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.82 % Allowed : 15.38 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.56 (0.24), residues: 1218 helix: -0.05 (0.27), residues: 376 sheet: -1.10 (0.28), residues: 326 loop : -1.64 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 243 HIS 0.009 0.001 HIS A 357 PHE 0.021 0.002 PHE R 280 TYR 0.022 0.002 TYR E 163 ARG 0.004 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 GLU cc_start: 0.6029 (OUTLIER) cc_final: 0.5662 (pm20) REVERT: B 8 ARG cc_start: 0.7208 (mpt-90) cc_final: 0.6993 (mtm-85) REVERT: B 10 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6764 (pm20) REVERT: B 225 HIS cc_start: 0.6521 (OUTLIER) cc_final: 0.5759 (m-70) REVERT: B 226 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.5981 (mt-10) REVERT: B 325 MET cc_start: 0.7732 (tpt) cc_final: 0.7503 (mmm) REVERT: E 77 ASN cc_start: 0.7076 (OUTLIER) cc_final: 0.6470 (m-40) REVERT: G 42 GLU cc_start: 0.7657 (pp20) cc_final: 0.7425 (tm-30) REVERT: N 39 GLN cc_start: 0.7225 (tt0) cc_final: 0.6698 (tt0) REVERT: R 170 ARG cc_start: 0.5314 (mmm160) cc_final: 0.4398 (mmt-90) REVERT: R 205 TYR cc_start: 0.3405 (OUTLIER) cc_final: 0.2453 (m-80) REVERT: R 294 GLU cc_start: 0.6323 (mp0) cc_final: 0.6004 (mp0) REVERT: R 348 ARG cc_start: 0.5167 (tpp-160) cc_final: 0.4891 (tpm170) outliers start: 40 outliers final: 27 residues processed: 200 average time/residue: 0.2399 time to fit residues: 64.8851 Evaluate side-chains 197 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 205 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN G 5 ASN N 3 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9978 Z= 0.166 Angle : 0.564 7.534 13522 Z= 0.297 Chirality : 0.041 0.154 1518 Planarity : 0.004 0.053 1712 Dihedral : 5.419 54.578 1366 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.82 % Allowed : 17.00 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.15 (0.24), residues: 1218 helix: 0.54 (0.27), residues: 364 sheet: -1.09 (0.28), residues: 341 loop : -1.39 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 243 HIS 0.007 0.001 HIS A 357 PHE 0.026 0.001 PHE R 280 TYR 0.010 0.001 TYR E 215 ARG 0.003 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.5927 (tp40) cc_final: 0.5009 (tm-30) REVERT: A 299 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5712 (pm20) REVERT: A 318 TYR cc_start: 0.7083 (t80) cc_final: 0.6619 (t80) REVERT: B 225 HIS cc_start: 0.6331 (OUTLIER) cc_final: 0.5897 (m-70) REVERT: B 290 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6513 (m-30) REVERT: N 39 GLN cc_start: 0.7123 (tt0) cc_final: 0.6530 (tt0) REVERT: R 170 ARG cc_start: 0.4909 (mmm160) cc_final: 0.4085 (mmt-90) REVERT: R 205 TYR cc_start: 0.3455 (OUTLIER) cc_final: 0.2280 (m-80) REVERT: R 294 GLU cc_start: 0.6252 (mp0) cc_final: 0.6001 (mp0) REVERT: R 404 PHE cc_start: 0.6361 (m-80) cc_final: 0.6156 (m-80) outliers start: 40 outliers final: 25 residues processed: 210 average time/residue: 0.2419 time to fit residues: 68.1104 Evaluate side-chains 195 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 205 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 279 ASN N 3 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9978 Z= 0.151 Angle : 0.564 9.831 13522 Z= 0.290 Chirality : 0.041 0.153 1518 Planarity : 0.003 0.048 1712 Dihedral : 4.855 54.463 1363 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.15 % Allowed : 19.01 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.90 (0.24), residues: 1218 helix: 0.77 (0.28), residues: 364 sheet: -0.84 (0.29), residues: 325 loop : -1.35 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.006 0.001 HIS A 357 PHE 0.025 0.001 PHE R 280 TYR 0.022 0.001 TYR R 289 ARG 0.006 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 TYR cc_start: 0.7025 (t80) cc_final: 0.6602 (t80) REVERT: B 225 HIS cc_start: 0.6190 (OUTLIER) cc_final: 0.5932 (m-70) REVERT: B 290 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6577 (m-30) REVERT: E 132 THR cc_start: 0.5982 (m) cc_final: 0.5666 (m) REVERT: N 39 GLN cc_start: 0.7105 (tt0) cc_final: 0.6555 (tt0) REVERT: R 170 ARG cc_start: 0.4908 (mmm160) cc_final: 0.4235 (mmt-90) REVERT: R 404 PHE cc_start: 0.6346 (m-80) cc_final: 0.6102 (m-80) outliers start: 33 outliers final: 25 residues processed: 203 average time/residue: 0.2299 time to fit residues: 63.3692 Evaluate side-chains 188 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.0370 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 279 ASN N 1 GLN N 3 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9978 Z= 0.156 Angle : 0.562 9.493 13522 Z= 0.292 Chirality : 0.041 0.155 1518 Planarity : 0.004 0.047 1712 Dihedral : 4.798 55.847 1363 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.82 % Allowed : 19.01 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.78 (0.24), residues: 1218 helix: 0.90 (0.28), residues: 364 sheet: -0.75 (0.29), residues: 323 loop : -1.31 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 243 HIS 0.005 0.001 HIS A 357 PHE 0.035 0.001 PHE R 280 TYR 0.023 0.001 TYR E 178 ARG 0.009 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 174 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.5813 (tp40) cc_final: 0.5116 (tm-30) REVERT: A 278 ASN cc_start: 0.7236 (m-40) cc_final: 0.7035 (m-40) REVERT: A 318 TYR cc_start: 0.6996 (t80) cc_final: 0.6594 (t80) REVERT: B 290 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6605 (m-30) REVERT: E 132 THR cc_start: 0.5898 (m) cc_final: 0.5579 (m) REVERT: G 37 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6223 (mt) REVERT: N 1 GLN cc_start: 0.5953 (OUTLIER) cc_final: 0.5599 (mp10) REVERT: N 39 GLN cc_start: 0.7147 (tt0) cc_final: 0.6592 (tt0) REVERT: N 105 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.5672 (ptt-90) REVERT: R 152 TYR cc_start: 0.5510 (t80) cc_final: 0.5235 (t80) REVERT: R 170 ARG cc_start: 0.4921 (mmm160) cc_final: 0.4117 (mmt-90) REVERT: R 205 TYR cc_start: 0.3148 (OUTLIER) cc_final: 0.2136 (m-80) REVERT: R 289 TYR cc_start: 0.4200 (t80) cc_final: 0.3733 (t80) REVERT: R 404 PHE cc_start: 0.6311 (m-80) cc_final: 0.6085 (m-80) outliers start: 40 outliers final: 26 residues processed: 199 average time/residue: 0.2360 time to fit residues: 63.9672 Evaluate side-chains 195 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 205 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 74 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 279 ASN N 3 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9978 Z= 0.278 Angle : 0.659 9.653 13522 Z= 0.343 Chirality : 0.044 0.155 1518 Planarity : 0.004 0.055 1712 Dihedral : 5.060 27.070 1361 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.44 % Allowed : 19.39 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.06 (0.24), residues: 1218 helix: 0.53 (0.27), residues: 366 sheet: -0.77 (0.29), residues: 323 loop : -1.49 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 243 HIS 0.006 0.001 HIS B 225 PHE 0.033 0.002 PHE R 280 TYR 0.018 0.002 TYR R 289 ARG 0.011 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.5851 (tp40) cc_final: 0.5019 (tm-30) REVERT: A 278 ASN cc_start: 0.7527 (m-40) cc_final: 0.7320 (m110) REVERT: A 318 TYR cc_start: 0.7178 (t80) cc_final: 0.6676 (t80) REVERT: B 43 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6859 (pt) REVERT: B 290 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6616 (m-30) REVERT: E 132 THR cc_start: 0.5935 (m) cc_final: 0.5620 (m) REVERT: N 1 GLN cc_start: 0.6055 (mp10) cc_final: 0.5802 (mp10) REVERT: N 39 GLN cc_start: 0.7146 (tt0) cc_final: 0.6535 (tt0) REVERT: N 105 ARG cc_start: 0.6171 (OUTLIER) cc_final: 0.5878 (ptt-90) REVERT: R 170 ARG cc_start: 0.5316 (mmm160) cc_final: 0.4463 (mmt-90) REVERT: R 205 TYR cc_start: 0.3350 (OUTLIER) cc_final: 0.2211 (m-80) REVERT: R 289 TYR cc_start: 0.4200 (t80) cc_final: 0.3872 (t80) REVERT: R 404 PHE cc_start: 0.6376 (m-80) cc_final: 0.6111 (m-80) outliers start: 36 outliers final: 27 residues processed: 184 average time/residue: 0.2354 time to fit residues: 58.7619 Evaluate side-chains 187 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 156 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 205 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 0.0570 chunk 102 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 0.0060 chunk 70 optimal weight: 0.8980 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 279 ASN N 3 GLN N 5 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9978 Z= 0.148 Angle : 0.577 9.584 13522 Z= 0.297 Chirality : 0.041 0.152 1518 Planarity : 0.004 0.053 1712 Dihedral : 4.517 24.983 1361 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.77 % Allowed : 20.44 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.70 (0.24), residues: 1218 helix: 0.93 (0.28), residues: 364 sheet: -0.68 (0.29), residues: 324 loop : -1.26 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.034 0.001 PHE R 280 TYR 0.018 0.001 TYR R 289 ARG 0.010 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 176 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.5903 (tp40) cc_final: 0.5141 (tm-30) REVERT: A 318 TYR cc_start: 0.7039 (t80) cc_final: 0.6599 (t80) REVERT: B 290 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6500 (m-30) REVERT: E 132 THR cc_start: 0.5833 (m) cc_final: 0.5513 (m) REVERT: N 39 GLN cc_start: 0.7039 (tt0) cc_final: 0.6487 (tt0) REVERT: N 105 ARG cc_start: 0.6244 (OUTLIER) cc_final: 0.5670 (ptt-90) REVERT: R 170 ARG cc_start: 0.5077 (mmm160) cc_final: 0.4252 (mmt-90) REVERT: R 289 TYR cc_start: 0.3862 (t80) cc_final: 0.3585 (t80) REVERT: R 404 PHE cc_start: 0.6352 (m-80) cc_final: 0.6114 (m-80) outliers start: 29 outliers final: 21 residues processed: 193 average time/residue: 0.2405 time to fit residues: 63.2660 Evaluate side-chains 187 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 0.0980 chunk 120 optimal weight: 0.0970 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 0.1980 chunk 58 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 102 optimal weight: 0.0570 chunk 29 optimal weight: 6.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 31 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9978 Z= 0.138 Angle : 0.563 9.562 13522 Z= 0.289 Chirality : 0.041 0.152 1518 Planarity : 0.004 0.050 1712 Dihedral : 4.247 24.070 1361 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.39 % Allowed : 20.82 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.52 (0.24), residues: 1218 helix: 1.13 (0.28), residues: 368 sheet: -0.67 (0.28), residues: 334 loop : -1.14 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.005 0.001 HIS A 357 PHE 0.033 0.001 PHE A 376 TYR 0.022 0.001 TYR E 178 ARG 0.005 0.000 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.5839 (tp40) cc_final: 0.5137 (tm-30) REVERT: A 318 TYR cc_start: 0.6974 (t80) cc_final: 0.6262 (t80) REVERT: B 146 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7304 (mm) REVERT: B 217 MET cc_start: 0.6122 (ppp) cc_final: 0.5639 (ptt) REVERT: B 290 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6432 (t0) REVERT: B 335 PHE cc_start: 0.7203 (m-10) cc_final: 0.6878 (m-10) REVERT: E 39 GLN cc_start: 0.5968 (tt0) cc_final: 0.5651 (tt0) REVERT: E 132 THR cc_start: 0.5740 (m) cc_final: 0.5396 (m) REVERT: G 37 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6198 (mt) REVERT: N 39 GLN cc_start: 0.6889 (tt0) cc_final: 0.6593 (tt0) REVERT: N 105 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5736 (ptp-170) REVERT: R 195 PHE cc_start: 0.3995 (t80) cc_final: 0.3578 (t80) REVERT: R 289 TYR cc_start: 0.3700 (t80) cc_final: 0.2826 (t80) REVERT: R 404 PHE cc_start: 0.6223 (m-80) cc_final: 0.5988 (m-80) outliers start: 25 outliers final: 17 residues processed: 205 average time/residue: 0.2427 time to fit residues: 66.9961 Evaluate side-chains 191 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 98 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 180 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.159837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.135426 restraints weight = 16219.523| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.92 r_work: 0.3827 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9978 Z= 0.163 Angle : 0.592 12.506 13522 Z= 0.300 Chirality : 0.041 0.155 1518 Planarity : 0.004 0.048 1712 Dihedral : 4.305 23.534 1361 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.48 % Allowed : 21.49 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.53 (0.24), residues: 1218 helix: 1.08 (0.28), residues: 373 sheet: -0.64 (0.28), residues: 329 loop : -1.15 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.036 0.001 PHE R 280 TYR 0.019 0.001 TYR B 85 ARG 0.006 0.000 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2412.58 seconds wall clock time: 44 minutes 1.33 seconds (2641.33 seconds total)