Starting phenix.real_space_refine on Tue Aug 6 06:21:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/08_2024/8x7a_38096_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/08_2024/8x7a_38096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/08_2024/8x7a_38096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/08_2024/8x7a_38096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/08_2024/8x7a_38096_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/08_2024/8x7a_38096_neut_trim.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 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 56 5.16 5 C 5028 2.51 5 N 1399 2.21 5 O 1466 1.98 5 H 7679 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 255": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 364": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 251": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 173": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15628 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3761 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 4782 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 851 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1849 Classifications: {'peptide': 128} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4357 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 14, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'Y9J': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.37, per 1000 atoms: 0.54 Number of scatterers: 15628 At special positions: 0 Unit cell: (81.03, 106.58, 128.48, 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 56 16.00 O 1466 8.00 N 1399 7.00 C 5028 6.00 H 7679 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 13.30 Conformation dependent library (CDL) restraints added in 1.6 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 42.0% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.678A pdb=" N ARG A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.256A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.804A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.890A pdb=" N TYR A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.502A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.704A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 19 through 41 removed outlier: 3.608A pdb=" N GLY R 27 " --> pdb=" O MET R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 66 removed outlier: 3.605A pdb=" N THR R 64 " --> pdb=" O ASP R 60 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE R 66 " --> pdb=" O LEU R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 78 removed outlier: 3.659A pdb=" N VAL R 71 " --> pdb=" O LEU R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 123 removed outlier: 4.768A pdb=" N CYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 129 Processing helix chain 'R' and resid 131 through 151 Proline residue: R 141 - end of helix Processing helix chain 'R' and resid 152 through 157 Processing helix chain 'R' and resid 183 through 221 Processing helix chain 'R' and resid 233 through 264 Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 271 through 283 Processing helix chain 'R' and resid 283 through 292 Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 296 through 307 Processing helix chain 'R' and resid 307 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.562A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.426A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.764A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.511A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.666A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.838A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.599A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.270A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.627A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL N 12 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 161 through 163 411 hydrogen bonds defined for protein. 1164 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: 5.56 Time building geometry restraints manager: 13.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.25: 8967 1.25 - 1.68: 6741 1.68 - 2.11: 78 2.11 - 2.54: 0 2.54 - 2.97: 1 Bond restraints: 15787 Sorted by residual: bond pdb=" C ALA B 203 " pdb=" N ASP B 205 " ideal model delta sigma weight residual 1.332 2.972 -1.639 1.40e-02 5.10e+03 1.37e+04 bond pdb=" C15 Y9J R 401 " pdb=" C21 Y9J R 401 " ideal model delta sigma weight residual 1.393 1.670 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C19 Y9J R 401 " pdb=" C20 Y9J R 401 " ideal model delta sigma weight residual 1.389 1.209 0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" C18 Y9J R 401 " pdb=" C19 Y9J R 401 " ideal model delta sigma weight residual 1.394 1.215 0.179 2.00e-02 2.50e+03 8.05e+01 bond pdb=" CA MET R 244 " pdb=" C MET R 244 " ideal model delta sigma weight residual 1.524 1.422 0.102 1.26e-02 6.30e+03 6.50e+01 ... (remaining 15782 not shown) Histogram of bond angle deviations from ideal: 59.61 - 77.69: 2 77.69 - 95.77: 0 95.77 - 113.85: 18591 113.85 - 131.93: 9745 131.93 - 150.01: 20 Bond angle restraints: 28358 Sorted by residual: angle pdb=" O ALA B 203 " pdb=" C ALA B 203 " pdb=" N ASP B 205 " ideal model delta sigma weight residual 122.27 59.61 62.66 1.16e+00 7.43e-01 2.92e+03 angle pdb=" CA ALA B 203 " pdb=" C ALA B 203 " pdb=" N ASP B 205 " ideal model delta sigma weight residual 118.79 150.01 -31.22 1.22e+00 6.72e-01 6.55e+02 angle pdb=" C ALA B 203 " pdb=" N ASP B 205 " pdb=" H ASP B 205 " ideal model delta sigma weight residual 124.38 66.43 57.95 3.00e+00 1.11e-01 3.73e+02 angle pdb=" C14 Y9J R 401 " pdb=" C15 Y9J R 401 " pdb=" C21 Y9J R 401 " ideal model delta sigma weight residual 121.72 143.69 -21.97 3.00e+00 1.11e-01 5.36e+01 angle pdb=" C ALA B 203 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta sigma weight residual 121.54 135.26 -13.72 1.91e+00 2.74e-01 5.16e+01 ... (remaining 28353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.03: 7234 21.03 - 42.07: 193 42.07 - 63.10: 73 63.10 - 84.14: 10 84.14 - 105.17: 1 Dihedral angle restraints: 7511 sinusoidal: 3974 harmonic: 3537 Sorted by residual: dihedral pdb=" CA ALA B 203 " pdb=" C ALA B 203 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta harmonic sigma weight residual -180.00 -74.83 -105.17 0 5.00e+00 4.00e-02 4.42e+02 dihedral pdb=" C MET R 244 " pdb=" N MET R 244 " pdb=" CA MET R 244 " pdb=" CB MET R 244 " ideal model delta harmonic sigma weight residual -122.60 -110.06 -12.54 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C ALA R 265 " pdb=" N ALA R 265 " pdb=" CA ALA R 265 " pdb=" CB ALA R 265 " ideal model delta harmonic sigma weight residual -122.60 -134.35 11.75 0 2.50e+00 1.60e-01 2.21e+01 ... (remaining 7508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1158 0.074 - 0.149: 86 0.149 - 0.223: 5 0.223 - 0.298: 1 0.298 - 0.372: 1 Chirality restraints: 1251 Sorted by residual: chirality pdb=" CA ALA R 265 " pdb=" N ALA R 265 " pdb=" C ALA R 265 " pdb=" CB ALA R 265 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA VAL R 25 " pdb=" N VAL R 25 " pdb=" C VAL R 25 " pdb=" CB VAL R 25 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C13 Y9J R 401 " pdb=" C12 Y9J R 401 " pdb=" C14 Y9J R 401 " pdb=" C9 Y9J R 401 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1248 not shown) Planarity restraints: 2422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 203 " 0.036 2.00e-02 2.50e+03 2.16e-01 4.66e+02 pdb=" N ASP B 205 " -0.362 2.00e-02 2.50e+03 pdb=" CA ASP B 205 " 0.141 2.00e-02 2.50e+03 pdb=" H ASP B 205 " 0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 203 " 0.182 2.00e-02 2.50e+03 1.90e-01 3.60e+02 pdb=" C ALA B 203 " -0.318 2.00e-02 2.50e+03 pdb=" O ALA B 203 " 0.062 2.00e-02 2.50e+03 pdb=" N ASP B 205 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 84 " 0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C LEU R 84 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU R 84 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA R 85 " 0.024 2.00e-02 2.50e+03 ... (remaining 2419 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 846 2.21 - 2.80: 32540 2.80 - 3.40: 42878 3.40 - 4.00: 55049 4.00 - 4.60: 86034 Nonbonded interactions: 217347 Sorted by model distance: nonbonded pdb=" O SER B 189 " pdb=" HG SER B 201 " model vdw 1.607 2.450 nonbonded pdb=" H THR B 221 " pdb=" OE2 GLU G 22 " model vdw 1.609 2.450 nonbonded pdb=" O ASP B 170 " pdb=" H GLY B 174 " model vdw 1.625 2.450 nonbonded pdb="HD21 ASN R 203 " pdb=" OG1 THR R 245 " model vdw 1.633 2.450 nonbonded pdb=" O LYS N 33 " pdb=" H CYS N 99 " model vdw 1.645 2.450 ... (remaining 217342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.700 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: 0.260 Extract box with map and model: 0.720 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 53.790 Find NCS groups from input model: 0.140 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.019 1.639 8108 Z= 1.554 Angle : 0.993 62.660 11001 Z= 0.688 Chirality : 0.040 0.372 1251 Planarity : 0.006 0.190 1419 Dihedral : 8.424 105.175 2894 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.12 % Allowed : 3.22 % Favored : 96.66 % Cbeta Deviations : 0.21 % 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: -0.63 (0.25), residues: 1028 helix: 0.95 (0.25), residues: 394 sheet: -0.65 (0.32), residues: 210 loop : -1.59 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 271 HIS 0.002 0.000 HIS B 142 PHE 0.005 0.001 PHE R 24 TYR 0.023 0.001 TYR R 75 ARG 0.002 0.000 ARG R 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 314 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 313 time to evaluate : 1.251 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: 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 outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 2.2720 time to fit residues: 756.9818 Evaluate side-chains 181 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN N 5 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8108 Z= 0.302 Angle : 0.615 6.404 11001 Z= 0.324 Chirality : 0.040 0.146 1251 Planarity : 0.005 0.063 1419 Dihedral : 5.243 74.091 1171 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Rotamer: Outliers : 3.09 % Allowed : 20.17 % Favored : 76.73 % 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: 0.50 (0.26), residues: 1030 helix: 2.03 (0.26), residues: 399 sheet: -0.66 (0.30), residues: 248 loop : -0.75 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS A 41 PHE 0.011 0.001 PHE N 68 TYR 0.023 0.002 TYR A 37 ARG 0.008 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 1.318 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.7107 (mtp) cc_final: 0.6764 (mtp) REVERT: N 60 TYR cc_start: 0.7255 (m-80) cc_final: 0.7019 (m-80) REVERT: R 41 ARG cc_start: 0.6630 (ptm-80) cc_final: 0.6410 (mpt180) REVERT: R 93 ASP cc_start: 0.7849 (m-30) cc_final: 0.7637 (m-30) outliers start: 25 outliers final: 12 residues processed: 190 average time/residue: 1.8767 time to fit residues: 384.5926 Evaluate side-chains 157 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 88 ASN B 340 ASN N 39 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 HIS R 284 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8108 Z= 0.240 Angle : 0.554 7.063 11001 Z= 0.287 Chirality : 0.039 0.156 1251 Planarity : 0.004 0.058 1419 Dihedral : 5.148 74.946 1171 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.47 % Allowed : 21.04 % Favored : 75.50 % 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: 0.78 (0.26), residues: 1030 helix: 2.30 (0.26), residues: 403 sheet: -0.61 (0.31), residues: 254 loop : -0.59 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS R 220 PHE 0.018 0.001 PHE R 102 TYR 0.016 0.001 TYR A 37 ARG 0.009 0.001 ARG R 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 1.279 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: R 86 ARG cc_start: 0.6019 (OUTLIER) cc_final: 0.4213 (mtm180) REVERT: R 93 ASP cc_start: 0.7887 (m-30) cc_final: 0.7669 (m-30) outliers start: 28 outliers final: 13 residues processed: 171 average time/residue: 1.9107 time to fit residues: 352.3475 Evaluate side-chains 155 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 234 GLU Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN R 220 HIS ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.6242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8108 Z= 0.444 Angle : 0.648 7.379 11001 Z= 0.343 Chirality : 0.041 0.147 1251 Planarity : 0.005 0.048 1419 Dihedral : 5.713 75.793 1171 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.21 % Allowed : 21.16 % Favored : 74.63 % 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 (0.26), residues: 1030 helix: 2.12 (0.26), residues: 402 sheet: -0.74 (0.31), residues: 252 loop : -0.61 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 36 HIS 0.007 0.002 HIS R 237 PHE 0.017 0.002 PHE R 102 TYR 0.020 0.002 TYR R 188 ARG 0.004 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 1.256 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: B 226 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: R 86 ARG cc_start: 0.6026 (OUTLIER) cc_final: 0.4293 (mtm180) REVERT: R 93 ASP cc_start: 0.7887 (m-30) cc_final: 0.7649 (m-30) outliers start: 34 outliers final: 12 residues processed: 168 average time/residue: 2.0970 time to fit residues: 377.6941 Evaluate side-chains 138 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.0170 chunk 40 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 0.0970 chunk 87 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN G 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8108 Z= 0.165 Angle : 0.555 7.178 11001 Z= 0.282 Chirality : 0.038 0.136 1251 Planarity : 0.004 0.045 1419 Dihedral : 5.168 72.283 1171 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.97 % Allowed : 22.77 % Favored : 74.26 % 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: 1.14 (0.27), residues: 1030 helix: 2.71 (0.26), residues: 397 sheet: -0.60 (0.32), residues: 241 loop : -0.33 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 290 HIS 0.004 0.001 HIS R 237 PHE 0.018 0.001 PHE R 102 TYR 0.013 0.001 TYR N 60 ARG 0.005 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.205 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: R 86 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.4317 (mtm180) REVERT: R 93 ASP cc_start: 0.7866 (m-30) cc_final: 0.7657 (m-30) outliers start: 24 outliers final: 12 residues processed: 159 average time/residue: 2.1282 time to fit residues: 362.7218 Evaluate side-chains 143 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 220 HIS Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 163 GLN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8108 Z= 0.260 Angle : 0.576 7.374 11001 Z= 0.296 Chirality : 0.039 0.200 1251 Planarity : 0.004 0.044 1419 Dihedral : 5.228 71.803 1171 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.97 % Allowed : 23.89 % Favored : 73.14 % 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: 1.16 (0.27), residues: 1030 helix: 2.76 (0.26), residues: 397 sheet: -0.60 (0.32), residues: 251 loop : -0.34 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.004 0.001 HIS R 237 PHE 0.014 0.001 PHE R 102 TYR 0.013 0.001 TYR R 188 ARG 0.009 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.377 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: R 86 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.4275 (mtm180) REVERT: R 93 ASP cc_start: 0.7866 (m-30) cc_final: 0.7644 (m-30) outliers start: 24 outliers final: 12 residues processed: 149 average time/residue: 2.1014 time to fit residues: 335.9008 Evaluate side-chains 141 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 220 HIS Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8108 Z= 0.237 Angle : 0.565 7.402 11001 Z= 0.292 Chirality : 0.038 0.140 1251 Planarity : 0.004 0.044 1419 Dihedral : 5.011 69.454 1171 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.23 % Allowed : 24.75 % Favored : 73.02 % 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: 1.20 (0.27), residues: 1030 helix: 2.80 (0.26), residues: 397 sheet: -0.49 (0.33), residues: 239 loop : -0.42 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.007 0.001 HIS R 237 PHE 0.015 0.001 PHE R 102 TYR 0.013 0.001 TYR R 188 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.241 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: R 86 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.4176 (mtm180) REVERT: R 93 ASP cc_start: 0.7854 (m-30) cc_final: 0.7619 (m-30) outliers start: 18 outliers final: 14 residues processed: 146 average time/residue: 2.0601 time to fit residues: 323.2550 Evaluate side-chains 143 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.7107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8108 Z= 0.320 Angle : 0.605 9.574 11001 Z= 0.315 Chirality : 0.039 0.154 1251 Planarity : 0.004 0.043 1419 Dihedral : 5.209 69.146 1171 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.60 % Allowed : 24.50 % Favored : 72.90 % 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: 1.03 (0.27), residues: 1030 helix: 2.53 (0.26), residues: 403 sheet: -0.54 (0.33), residues: 244 loop : -0.43 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 36 HIS 0.007 0.001 HIS R 237 PHE 0.016 0.002 PHE R 102 TYR 0.016 0.002 TYR R 188 ARG 0.010 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.263 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: R 86 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.4167 (mtm180) REVERT: R 93 ASP cc_start: 0.7853 (m-30) cc_final: 0.7599 (m-30) REVERT: R 138 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6817 (tt) outliers start: 21 outliers final: 15 residues processed: 146 average time/residue: 2.4101 time to fit residues: 374.6654 Evaluate side-chains 138 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 234 GLU Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8108 Z= 0.254 Angle : 0.587 9.707 11001 Z= 0.303 Chirality : 0.039 0.140 1251 Planarity : 0.004 0.047 1419 Dihedral : 5.096 68.582 1171 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.35 % Allowed : 24.88 % Favored : 72.77 % 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: 1.13 (0.27), residues: 1030 helix: 2.65 (0.26), residues: 403 sheet: -0.48 (0.34), residues: 229 loop : -0.45 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.006 0.001 HIS R 237 PHE 0.017 0.001 PHE R 102 TYR 0.013 0.001 TYR R 188 ARG 0.006 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.278 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: B 42 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6236 (tmm-80) REVERT: G 62 ARG cc_start: 0.5421 (pmt170) cc_final: 0.5002 (ptt-90) REVERT: R 86 ARG cc_start: 0.6021 (OUTLIER) cc_final: 0.4180 (mtm180) REVERT: R 93 ASP cc_start: 0.7869 (m-30) cc_final: 0.7602 (m-30) outliers start: 19 outliers final: 13 residues processed: 140 average time/residue: 2.4257 time to fit residues: 361.3035 Evaluate side-chains 138 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN N 82 GLN ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8108 Z= 0.244 Angle : 0.596 9.883 11001 Z= 0.306 Chirality : 0.039 0.142 1251 Planarity : 0.004 0.044 1419 Dihedral : 5.030 67.657 1171 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.10 % Allowed : 25.37 % Favored : 72.52 % 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: 1.14 (0.27), residues: 1030 helix: 2.71 (0.26), residues: 403 sheet: -0.49 (0.33), residues: 229 loop : -0.48 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.006 0.001 HIS R 237 PHE 0.018 0.001 PHE R 102 TYR 0.012 0.001 TYR A 37 ARG 0.006 0.000 ARG G 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 53 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue SER 65 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.323 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: G 62 ARG cc_start: 0.5589 (pmt170) cc_final: 0.5287 (ptt-90) REVERT: R 86 ARG cc_start: 0.6049 (OUTLIER) cc_final: 0.4150 (mtm180) REVERT: R 93 ASP cc_start: 0.7900 (m-30) cc_final: 0.7629 (m-30) outliers start: 17 outliers final: 14 residues processed: 136 average time/residue: 2.3591 time to fit residues: 342.7984 Evaluate side-chains 135 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.116187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.085933 restraints weight = 48577.397| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.48 r_work: 0.3281 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8108 Z= 0.208 Angle : 0.583 9.840 11001 Z= 0.299 Chirality : 0.038 0.140 1251 Planarity : 0.004 0.044 1419 Dihedral : 4.942 66.322 1171 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.10 % Allowed : 25.37 % Favored : 72.52 % 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: 1.24 (0.27), residues: 1030 helix: 2.83 (0.26), residues: 403 sheet: -0.34 (0.35), residues: 204 loop : -0.56 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.005 0.001 HIS R 237 PHE 0.017 0.001 PHE R 102 TYR 0.011 0.001 TYR A 37 ARG 0.017 0.001 ARG G 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7142.48 seconds wall clock time: 123 minutes 24.84 seconds (7404.84 seconds total)