Starting phenix.real_space_refine on Sun Jul 21 20:22:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/07_2024/8x7a_38096_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/07_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_38096/07_2024/8x7a_38096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/07_2024/8x7a_38096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/07_2024/8x7a_38096_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7a_38096/07_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-5388/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: 7.67, per 1000 atoms: 0.49 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: 12.44 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: 1.43 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: 5.28 Time building geometry restraints manager: 13.03 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 1.850 nonbonded pdb=" H THR B 221 " pdb=" OE2 GLU G 22 " model vdw 1.609 1.850 nonbonded pdb=" O ASP B 170 " pdb=" H GLY B 174 " model vdw 1.625 1.850 nonbonded pdb="HD21 ASN R 203 " pdb=" OG1 THR R 245 " model vdw 1.633 1.850 nonbonded pdb=" O LYS N 33 " pdb=" H CYS N 99 " model vdw 1.645 1.850 ... (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 ========== 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: 3.100 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: 0.240 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 51.270 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.060 ------------------------------------------------------------------------------- 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 : 1.267 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: 2.2791 time to fit residues: 758.5116 Evaluate side-chains 181 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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: 1.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 26 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8108 Z= 0.233 Angle : 0.561 6.217 11001 Z= 0.291 Chirality : 0.039 0.163 1251 Planarity : 0.004 0.055 1419 Dihedral : 4.825 68.539 1171 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.04 % Favored : 97.86 % Rotamer: Outliers : 3.22 % Allowed : 20.30 % Favored : 76.49 % 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: 0.61 (0.26), residues: 1030 helix: 2.13 (0.27), residues: 399 sheet: -0.47 (0.30), residues: 246 loop : -0.79 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS A 41 PHE 0.009 0.001 PHE N 68 TYR 0.018 0.001 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 203 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 177 time to evaluate : 1.246 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: N 60 TYR cc_start: 0.7120 (m-80) cc_final: 0.6875 (m-80) REVERT: R 41 ARG cc_start: 0.6677 (ptm-80) cc_final: 0.6446 (mpt180) outliers start: 26 outliers final: 15 residues processed: 193 average time/residue: 1.8864 time to fit residues: 392.4488 Evaluate side-chains 166 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU 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 228 ASP Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 106 SER 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: 2.9990 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 88 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8108 Z= 0.232 Angle : 0.542 6.960 11001 Z= 0.279 Chirality : 0.038 0.147 1251 Planarity : 0.004 0.056 1419 Dihedral : 4.841 69.340 1171 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.34 % Allowed : 21.16 % 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: 0.91 (0.26), residues: 1030 helix: 2.39 (0.26), residues: 403 sheet: -0.38 (0.31), residues: 252 loop : -0.63 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 237 PHE 0.016 0.001 PHE R 102 TYR 0.015 0.001 TYR A 37 ARG 0.005 0.000 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: 27 poor density : 157 time to evaluate : 1.214 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: R 86 ARG cc_start: 0.6040 (OUTLIER) cc_final: 0.4234 (mtm180) outliers start: 27 outliers final: 17 residues processed: 176 average time/residue: 1.9387 time to fit residues: 367.6647 Evaluate side-chains 159 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 289 GLU 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 B residue 228 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 106 SER 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 267 ASP 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: 8.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 213 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: 0.7654 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 8108 Z= 0.465 Angle : 0.662 9.022 11001 Z= 0.354 Chirality : 0.042 0.145 1251 Planarity : 0.005 0.063 1419 Dihedral : 5.755 69.104 1171 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.83 % Rotamer: Outliers : 5.20 % Allowed : 20.42 % Favored : 74.38 % 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: 2.06 (0.26), residues: 402 sheet: -0.56 (0.32), residues: 241 loop : -0.69 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 36 HIS 0.008 0.002 HIS A 41 PHE 0.018 0.002 PHE R 102 TYR 0.021 0.002 TYR R 125 ARG 0.005 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 181 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 139 time to evaluate : 1.106 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: 0.5966 (OUTLIER) cc_final: 0.4243 (mtm180) REVERT: R 138 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6740 (tt) outliers start: 42 outliers final: 18 residues processed: 164 average time/residue: 2.0005 time to fit residues: 352.4296 Evaluate side-chains 148 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU 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 223 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 ARG Chi-restraints excluded: chain R residue 106 SER 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 252 SER Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 302 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 0.0980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN G 18 GLN ** 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: 0.7581 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8108 Z= 0.184 Angle : 0.537 5.385 11001 Z= 0.277 Chirality : 0.038 0.139 1251 Planarity : 0.004 0.042 1419 Dihedral : 5.046 66.425 1171 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.97 % Allowed : 22.28 % Favored : 74.75 % 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 (0.26), residues: 1030 helix: 2.62 (0.26), residues: 398 sheet: -0.38 (0.32), residues: 237 loop : -0.45 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS R 237 PHE 0.018 0.001 PHE R 102 TYR 0.013 0.001 TYR A 37 ARG 0.005 0.000 ARG G 13 *********************** 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 161 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 ARG cc_start: 0.6045 (OUTLIER) cc_final: 0.4353 (mtm180) REVERT: R 138 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6754 (tt) outliers start: 24 outliers final: 13 residues processed: 153 average time/residue: 2.0883 time to fit residues: 343.3852 Evaluate side-chains 142 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 289 GLU 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 G residue 22 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 70 ILE 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 252 SER Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN G 18 GLN ** 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: 0.7619 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8108 Z= 0.277 Angle : 0.567 6.873 11001 Z= 0.294 Chirality : 0.039 0.227 1251 Planarity : 0.004 0.041 1419 Dihedral : 5.045 66.904 1171 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.09 % Allowed : 23.02 % Favored : 73.89 % 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: 1.11 (0.27), residues: 1030 helix: 2.55 (0.26), residues: 404 sheet: -0.41 (0.32), residues: 241 loop : -0.41 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.005 0.001 HIS R 237 PHE 0.014 0.001 PHE R 102 TYR 0.014 0.001 TYR R 188 ARG 0.005 0.000 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 152 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 1.248 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: 0.5920 (OUTLIER) cc_final: 0.4273 (mtm180) REVERT: R 138 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6762 (tt) outliers start: 25 outliers final: 14 residues processed: 144 average time/residue: 2.1469 time to fit residues: 330.8638 Evaluate side-chains 139 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU 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 G residue 57 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 68 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 0.0010 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN ** 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: 0.7574 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8108 Z= 0.168 Angle : 0.530 8.480 11001 Z= 0.269 Chirality : 0.038 0.136 1251 Planarity : 0.004 0.040 1419 Dihedral : 4.751 65.409 1171 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.85 % Allowed : 23.02 % Favored : 74.13 % 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: 1.42 (0.27), residues: 1030 helix: 2.87 (0.26), residues: 398 sheet: -0.22 (0.33), residues: 233 loop : -0.30 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS R 237 PHE 0.016 0.001 PHE R 102 TYR 0.012 0.001 TYR A 37 ARG 0.007 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 154 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.130 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: R 86 ARG cc_start: 0.5926 (OUTLIER) cc_final: 0.4212 (mtm180) REVERT: R 138 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6720 (tt) outliers start: 23 outliers final: 15 residues processed: 148 average time/residue: 2.0775 time to fit residues: 329.6162 Evaluate side-chains 138 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 68 SER 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 178 GLN Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain R residue 255 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 GLN ** 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: 0.7612 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8108 Z= 0.247 Angle : 0.557 8.641 11001 Z= 0.286 Chirality : 0.038 0.182 1251 Planarity : 0.004 0.039 1419 Dihedral : 4.826 64.865 1171 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.10 % Allowed : 23.89 % Favored : 74.01 % 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: 1.37 (0.27), residues: 1030 helix: 2.79 (0.26), residues: 398 sheet: -0.20 (0.33), residues: 233 loop : -0.30 (0.31), residues: 399 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 0.014 0.001 PHE R 102 TYR 0.014 0.001 TYR R 188 ARG 0.008 0.000 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 141 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.237 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: 0.5897 (OUTLIER) cc_final: 0.4183 (mtm180) REVERT: R 138 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6738 (tt) outliers start: 17 outliers final: 13 residues processed: 139 average time/residue: 2.3737 time to fit residues: 351.7126 Evaluate side-chains 138 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU 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 226 GLU 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 R residue 68 SER 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 252 SER Chi-restraints excluded: chain R residue 255 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 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: 0.7601 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8108 Z= 0.204 Angle : 0.546 9.571 11001 Z= 0.279 Chirality : 0.038 0.136 1251 Planarity : 0.004 0.039 1419 Dihedral : 4.736 64.554 1171 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.98 % Allowed : 24.01 % Favored : 74.01 % 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: 1.47 (0.27), residues: 1030 helix: 2.91 (0.26), residues: 397 sheet: -0.18 (0.33), residues: 234 loop : -0.27 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS R 237 PHE 0.015 0.001 PHE R 102 TYR 0.012 0.001 TYR A 37 ARG 0.004 0.000 ARG R 302 *********************** 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 143 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.250 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: 0.5937 (OUTLIER) cc_final: 0.4150 (ttm170) REVERT: R 138 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6720 (tt) outliers start: 16 outliers final: 13 residues processed: 141 average time/residue: 2.3339 time to fit residues: 350.4752 Evaluate side-chains 137 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU 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 226 GLU 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 R residue 68 SER 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 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: 5.9990 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.7612 moved from start: 0.7016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8108 Z= 0.225 Angle : 0.560 9.807 11001 Z= 0.285 Chirality : 0.038 0.142 1251 Planarity : 0.004 0.038 1419 Dihedral : 4.717 62.775 1171 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.86 % Allowed : 24.50 % Favored : 73.64 % 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: 1.44 (0.27), residues: 1030 helix: 2.85 (0.26), residues: 403 sheet: -0.17 (0.33), residues: 234 loop : -0.32 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.007 0.001 HIS R 237 PHE 0.014 0.001 PHE R 102 TYR 0.012 0.001 TYR R 188 ARG 0.008 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 140 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.214 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: 0.5961 (OUTLIER) cc_final: 0.4150 (ttm170) REVERT: R 138 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6717 (tt) outliers start: 15 outliers final: 13 residues processed: 138 average time/residue: 2.2989 time to fit residues: 338.5394 Evaluate side-chains 138 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU 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 226 GLU 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 R residue 68 SER 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 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: 0.5980 chunk 11 optimal weight: 1.9990 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: 3.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.115763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.084992 restraints weight = 48592.376| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.50 r_work: 0.3254 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8108 Z= 0.205 Angle : 0.558 9.866 11001 Z= 0.285 Chirality : 0.038 0.141 1251 Planarity : 0.004 0.038 1419 Dihedral : 4.681 62.785 1171 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.98 % Allowed : 24.01 % Favored : 74.01 % 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: 1.45 (0.27), residues: 1030 helix: 2.85 (0.26), residues: 403 sheet: -0.10 (0.34), residues: 223 loop : -0.34 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.010 0.001 HIS R 237 PHE 0.014 0.001 PHE R 102 TYR 0.012 0.001 TYR A 37 ARG 0.011 0.000 ARG G 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7213.70 seconds wall clock time: 124 minutes 39.62 seconds (7479.62 seconds total)