Starting phenix.real_space_refine on Mon Mar 11 03:45:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2i_0331/03_2024/6i2i_0331_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2i_0331/03_2024/6i2i_0331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2i_0331/03_2024/6i2i_0331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2i_0331/03_2024/6i2i_0331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2i_0331/03_2024/6i2i_0331_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2i_0331/03_2024/6i2i_0331_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.016 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 4303 2.51 5 N 1157 2.21 5 O 1316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6830 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3346 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {' MG': 1, 'G2P': 1, 'TA1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.05, per 1000 atoms: 0.59 Number of scatterers: 6830 At special positions: 0 Unit cell: (75.35, 71.24, 115.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 6 15.00 Mg 2 11.99 O 1316 8.00 N 1157 7.00 C 4303 6.00 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: 3.03 Conformation dependent library (CDL) restraints added in 1.1 seconds 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 7 sheets defined 39.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 11 through 27 removed outlier: 3.648A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS A 25 " --> pdb=" O TRP A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.704A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 103 through 106 No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 111 through 126 removed outlier: 5.047A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 161 removed outlier: 3.551A pdb=" N PHE A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 193 removed outlier: 4.688A pdb=" N SER A 187 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 188 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 189 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 190 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 191 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A 192 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 210 No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 212 through 215 No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.693A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.558A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 293 through 296 removed outlier: 3.595A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.767A pdb=" N ASN A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 389 through 396 removed outlier: 3.605A pdb=" N HIS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 436 removed outlier: 3.650A pdb=" N ARG A 422 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 26 removed outlier: 3.771A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 25 " --> pdb=" O TRP B 21 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 44 No H-bonds generated for 'chain 'B' and resid 41 through 44' Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 80 removed outlier: 3.602A pdb=" N SER B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 115 through 125 removed outlier: 4.309A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'B' and resid 152 through 160 removed outlier: 4.050A pdb=" N GLU B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 188 No H-bonds generated for 'chain 'B' and resid 185 through 188' Processing helix chain 'B' and resid 192 through 195 No H-bonds generated for 'chain 'B' and resid 192 through 195' Processing helix chain 'B' and resid 206 through 214 removed outlier: 3.610A pdb=" N TYR B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 238 removed outlier: 4.111A pdb=" N HIS B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA B 233 " --> pdb=" O HIS B 229 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.797A pdb=" N ASN B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 295 removed outlier: 3.779A pdb=" N GLN B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.776A pdb=" N GLN B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 383 through 400 removed outlier: 4.147A pdb=" N PHE B 388 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 392 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU B 393 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 395 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 397 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE B 399 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.795A pdb=" N GLY B 410 " --> pdb=" O HIS B 406 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 411' Processing helix chain 'B' and resid 416 through 432 removed outlier: 3.514A pdb=" N GLU B 420 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU B 422 " --> pdb=" O PHE B 418 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 429 " --> pdb=" O MET B 425 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.589A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 268 through 270 Processing sheet with id= D, first strand: chain 'A' and resid 353 through 356 removed outlier: 6.939A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASN A 356 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR A 319 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.959A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU B 200 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N SER B 170 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 172 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE B 204 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 53 through 56 Processing sheet with id= G, first strand: chain 'B' and resid 352 through 356 removed outlier: 3.793A pdb=" N LYS B 352 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B 380 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL B 315 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 378 " --> pdb=" O VAL B 315 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 342 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: 1.65 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1172 1.32 - 1.44: 1885 1.44 - 1.56: 3844 1.56 - 1.69: 15 1.69 - 1.81: 74 Bond restraints: 6990 Sorted by residual: bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.585 0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" O5' G2P B 501 " pdb=" PA G2P B 501 " ideal model delta sigma weight residual 1.656 1.574 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.463 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C01 TA1 B 503 " pdb=" C45 TA1 B 503 " ideal model delta sigma weight residual 1.553 1.615 -0.062 2.00e-02 2.50e+03 9.71e+00 bond pdb=" C3A G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 1.850 1.796 0.054 2.00e-02 2.50e+03 7.35e+00 ... (remaining 6985 not shown) Histogram of bond angle deviations from ideal: 84.77 - 94.61: 4 94.61 - 104.45: 145 104.45 - 114.30: 4043 114.30 - 124.14: 5146 124.14 - 133.99: 174 Bond angle restraints: 9512 Sorted by residual: angle pdb=" C14 TA1 B 503 " pdb=" C11 TA1 B 503 " pdb=" O04 TA1 B 503 " ideal model delta sigma weight residual 119.42 102.12 17.30 3.00e+00 1.11e-01 3.33e+01 angle pdb=" C10 TA1 B 503 " pdb=" C18 TA1 B 503 " pdb=" C20 TA1 B 503 " ideal model delta sigma weight residual 104.78 120.74 -15.96 3.00e+00 1.11e-01 2.83e+01 angle pdb=" O2A G2P B 501 " pdb=" PA G2P B 501 " pdb=" O5' G2P B 501 " ideal model delta sigma weight residual 107.71 121.30 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" O2' G2P B 501 " ideal model delta sigma weight residual 116.29 103.49 12.80 3.00e+00 1.11e-01 1.82e+01 angle pdb=" O1A G2P B 501 " pdb=" PA G2P B 501 " pdb=" O2A G2P B 501 " ideal model delta sigma weight residual 117.48 105.46 12.02 3.00e+00 1.11e-01 1.60e+01 ... (remaining 9507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.48: 4147 33.48 - 66.97: 57 66.97 - 100.45: 12 100.45 - 133.93: 13 133.93 - 167.41: 7 Dihedral angle restraints: 4236 sinusoidal: 1765 harmonic: 2471 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -123.32 -167.41 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -53.53 158.12 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 131.59 142.53 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 4233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 790 0.072 - 0.145: 226 0.145 - 0.217: 21 0.217 - 0.289: 2 0.289 - 0.361: 3 Chirality restraints: 1042 Sorted by residual: chirality pdb=" C10 TA1 B 503 " pdb=" C02 TA1 B 503 " pdb=" C11 TA1 B 503 " pdb=" C18 TA1 B 503 " both_signs ideal model delta sigma weight residual False 2.54 2.18 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C26 TA1 B 503 " pdb=" C25 TA1 B 503 " pdb=" C43 TA1 B 503 " pdb=" O11 TA1 B 503 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL A 182 " pdb=" CA VAL A 182 " pdb=" CG1 VAL A 182 " pdb=" CG2 VAL A 182 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 1039 not shown) Planarity restraints: 1231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 TA1 B 503 " 0.004 2.00e-02 2.50e+03 3.19e-02 1.79e+01 pdb=" C04 TA1 B 503 " 0.046 2.00e-02 2.50e+03 pdb=" C05 TA1 B 503 " -0.057 2.00e-02 2.50e+03 pdb=" C06 TA1 B 503 " 0.021 2.00e-02 2.50e+03 pdb=" C07 TA1 B 503 " 0.023 2.00e-02 2.50e+03 pdb=" C08 TA1 B 503 " -0.026 2.00e-02 2.50e+03 pdb=" C09 TA1 B 503 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 TA1 B 503 " 0.053 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C04 TA1 B 503 " -0.015 2.00e-02 2.50e+03 pdb=" O02 TA1 B 503 " -0.017 2.00e-02 2.50e+03 pdb=" O03 TA1 B 503 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 31 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO B 32 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.038 5.00e-02 4.00e+02 ... (remaining 1228 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 97 2.59 - 3.17: 5601 3.17 - 3.75: 10446 3.75 - 4.32: 14934 4.32 - 4.90: 23702 Nonbonded interactions: 54780 Sorted by model distance: nonbonded pdb=" O2G G2P B 501 " pdb="MG MG B 502 " model vdw 2.019 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.064 2.170 nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 2.107 2.170 nonbonded pdb=" OD1 ASN B 101 " pdb=" O3G G2P B 501 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU B 27 " pdb=" OG SER B 236 " model vdw 2.275 2.440 ... (remaining 54775 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 21.600 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 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 : 0.009 0.131 6990 Z= 0.593 Angle : 1.175 17.302 9512 Z= 0.583 Chirality : 0.065 0.361 1042 Planarity : 0.008 0.069 1231 Dihedral : 16.637 167.414 2652 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.28 % Allowed : 2.21 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -5.22 (0.21), residues: 850 helix: -4.20 (0.14), residues: 330 sheet: -3.16 (0.39), residues: 132 loop : -2.73 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 346 HIS 0.014 0.003 HIS B 229 PHE 0.028 0.004 PHE A 351 TYR 0.036 0.004 TYR B 312 ARG 0.009 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7601 (tt0) REVERT: A 176 GLN cc_start: 0.8098 (mm110) cc_final: 0.7790 (mm110) REVERT: A 302 MET cc_start: 0.8358 (mmp) cc_final: 0.7880 (mmm) REVERT: A 313 MET cc_start: 0.7282 (mtt) cc_final: 0.7031 (mtp) REVERT: A 388 TRP cc_start: 0.5549 (m-10) cc_final: 0.5184 (m-10) REVERT: A 397 LEU cc_start: 0.8594 (mt) cc_final: 0.8384 (mt) REVERT: B 1 MET cc_start: 0.6986 (mmt) cc_final: 0.6196 (tmm) REVERT: B 6 HIS cc_start: 0.7620 (t70) cc_final: 0.7091 (t-170) REVERT: B 37 HIS cc_start: 0.7721 (m90) cc_final: 0.7375 (m170) REVERT: B 110 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7779 (tt0) REVERT: B 247 GLN cc_start: 0.8092 (mt0) cc_final: 0.7853 (tt0) REVERT: B 282 GLN cc_start: 0.8400 (mm110) cc_final: 0.7598 (mp10) REVERT: B 300 ASN cc_start: 0.8709 (t160) cc_final: 0.8207 (m-40) REVERT: B 325 MET cc_start: 0.8389 (mmm) cc_final: 0.8093 (tpt) REVERT: B 330 GLU cc_start: 0.8808 (tt0) cc_final: 0.8487 (tp30) REVERT: B 333 LEU cc_start: 0.9134 (tp) cc_final: 0.8767 (tp) REVERT: B 417 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7580 (tp30) outliers start: 2 outliers final: 1 residues processed: 220 average time/residue: 0.2121 time to fit residues: 60.0324 Evaluate side-chains 145 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 88 HIS A 258 ASN A 372 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN B 249 ASN B 258 ASN B 300 ASN B 337 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6990 Z= 0.234 Angle : 0.667 8.958 9512 Z= 0.328 Chirality : 0.048 0.474 1042 Planarity : 0.006 0.063 1231 Dihedral : 14.129 172.908 1084 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.17 % Allowed : 10.76 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.98 (0.25), residues: 850 helix: -2.98 (0.22), residues: 337 sheet: -2.59 (0.41), residues: 137 loop : -2.13 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 346 HIS 0.005 0.001 HIS A 61 PHE 0.022 0.002 PHE A 395 TYR 0.018 0.002 TYR B 312 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6822 (mt) REVERT: A 176 GLN cc_start: 0.8238 (mm110) cc_final: 0.7880 (mm110) REVERT: A 280 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6790 (tptt) REVERT: A 313 MET cc_start: 0.7456 (mtt) cc_final: 0.7229 (mtp) REVERT: A 397 LEU cc_start: 0.8795 (mt) cc_final: 0.8584 (mt) REVERT: A 413 MET cc_start: 0.7009 (tpt) cc_final: 0.5791 (mtp) REVERT: B 6 HIS cc_start: 0.7439 (t70) cc_final: 0.7234 (t-170) REVERT: B 26 ASP cc_start: 0.8257 (m-30) cc_final: 0.7738 (m-30) REVERT: B 110 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7631 (tt0) REVERT: B 113 GLU cc_start: 0.8001 (mp0) cc_final: 0.7732 (mp0) REVERT: B 124 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8082 (tttt) REVERT: B 163 ASP cc_start: 0.7920 (p0) cc_final: 0.7556 (p0) REVERT: B 247 GLN cc_start: 0.8077 (mt0) cc_final: 0.7791 (tt0) REVERT: B 372 LYS cc_start: 0.8500 (ttpp) cc_final: 0.8052 (ttpp) REVERT: B 417 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7608 (tp30) outliers start: 23 outliers final: 16 residues processed: 174 average time/residue: 0.1967 time to fit residues: 44.6853 Evaluate side-chains 151 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 329 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6990 Z= 0.224 Angle : 0.608 7.994 9512 Z= 0.301 Chirality : 0.046 0.288 1042 Planarity : 0.005 0.061 1231 Dihedral : 13.005 171.785 1084 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.45 % Allowed : 12.83 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.39 (0.26), residues: 850 helix: -2.44 (0.24), residues: 346 sheet: -2.40 (0.42), residues: 135 loop : -1.78 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 388 HIS 0.004 0.001 HIS A 8 PHE 0.021 0.002 PHE A 395 TYR 0.018 0.002 TYR B 312 ARG 0.004 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6784 (mt) REVERT: A 176 GLN cc_start: 0.8206 (mm110) cc_final: 0.7863 (mm110) REVERT: A 280 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6725 (tptt) REVERT: A 302 MET cc_start: 0.8459 (mmp) cc_final: 0.8040 (mmm) REVERT: A 313 MET cc_start: 0.7260 (mtt) cc_final: 0.6966 (mtp) REVERT: A 413 MET cc_start: 0.7206 (tpt) cc_final: 0.5954 (mtp) REVERT: B 6 HIS cc_start: 0.7472 (t70) cc_final: 0.7266 (t-170) REVERT: B 26 ASP cc_start: 0.8177 (m-30) cc_final: 0.7686 (m-30) REVERT: B 110 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7606 (tt0) REVERT: B 113 GLU cc_start: 0.8001 (mp0) cc_final: 0.7485 (mp0) REVERT: B 124 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8142 (tttt) REVERT: B 163 ASP cc_start: 0.7985 (p0) cc_final: 0.7660 (p0) REVERT: B 167 ASN cc_start: 0.7444 (m-40) cc_final: 0.7116 (m110) REVERT: B 247 GLN cc_start: 0.8059 (mt0) cc_final: 0.7751 (tt0) REVERT: B 372 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8092 (ttpp) REVERT: B 398 MET cc_start: 0.7407 (mtp) cc_final: 0.7069 (mtt) outliers start: 25 outliers final: 19 residues processed: 153 average time/residue: 0.1904 time to fit residues: 38.7606 Evaluate side-chains 150 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 256 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6990 Z= 0.225 Angle : 0.591 8.496 9512 Z= 0.292 Chirality : 0.046 0.257 1042 Planarity : 0.005 0.061 1231 Dihedral : 12.729 172.708 1084 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.86 % Allowed : 14.34 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.91 (0.27), residues: 850 helix: -1.97 (0.25), residues: 343 sheet: -2.25 (0.43), residues: 135 loop : -1.56 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 388 HIS 0.007 0.001 HIS A 107 PHE 0.023 0.002 PHE A 395 TYR 0.017 0.002 TYR B 312 ARG 0.003 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8127 (mm110) cc_final: 0.7914 (mm110) REVERT: A 280 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6687 (tptt) REVERT: A 313 MET cc_start: 0.7190 (mtt) cc_final: 0.6827 (mtp) REVERT: A 372 GLN cc_start: 0.7618 (mt0) cc_final: 0.7349 (mp10) REVERT: A 413 MET cc_start: 0.7249 (tpt) cc_final: 0.5946 (mtp) REVERT: A 415 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6691 (tm-30) REVERT: B 6 HIS cc_start: 0.7538 (t70) cc_final: 0.7287 (t-170) REVERT: B 26 ASP cc_start: 0.8137 (m-30) cc_final: 0.7668 (m-30) REVERT: B 113 GLU cc_start: 0.7774 (mp0) cc_final: 0.7442 (mp0) REVERT: B 124 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8120 (tttt) REVERT: B 136 GLN cc_start: 0.7902 (mt0) cc_final: 0.7536 (mt0) REVERT: B 163 ASP cc_start: 0.8082 (p0) cc_final: 0.7747 (p0) REVERT: B 167 ASN cc_start: 0.7596 (m-40) cc_final: 0.7303 (m110) REVERT: B 247 GLN cc_start: 0.8086 (mt0) cc_final: 0.7780 (tt0) REVERT: B 325 MET cc_start: 0.8800 (tpp) cc_final: 0.8289 (mmm) REVERT: B 372 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8042 (ttpp) REVERT: B 398 MET cc_start: 0.7458 (mtp) cc_final: 0.7044 (mtt) outliers start: 28 outliers final: 20 residues processed: 149 average time/residue: 0.1806 time to fit residues: 36.3416 Evaluate side-chains 142 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 20 optimal weight: 0.0270 chunk 27 optimal weight: 0.0670 overall best weight: 4.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6990 Z= 0.216 Angle : 0.572 8.161 9512 Z= 0.282 Chirality : 0.045 0.221 1042 Planarity : 0.004 0.060 1231 Dihedral : 12.545 173.225 1084 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.28 % Allowed : 15.03 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.62 (0.28), residues: 850 helix: -1.62 (0.26), residues: 345 sheet: -2.15 (0.43), residues: 132 loop : -1.50 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 388 HIS 0.005 0.001 HIS A 88 PHE 0.024 0.002 PHE A 395 TYR 0.017 0.001 TYR B 312 ARG 0.002 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 0.798 Fit side-chains REVERT: A 155 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8378 (mm-30) REVERT: A 176 GLN cc_start: 0.8225 (mm110) cc_final: 0.7962 (mm110) REVERT: A 245 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6690 (p0) REVERT: A 280 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6720 (tptt) REVERT: A 313 MET cc_start: 0.7156 (mtt) cc_final: 0.6788 (mtp) REVERT: A 413 MET cc_start: 0.7314 (tpt) cc_final: 0.6212 (mtp) REVERT: A 415 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6698 (tm-30) REVERT: B 6 HIS cc_start: 0.7500 (t70) cc_final: 0.7218 (t-170) REVERT: B 26 ASP cc_start: 0.8089 (m-30) cc_final: 0.7738 (m-30) REVERT: B 31 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: B 110 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7359 (tt0) REVERT: B 113 GLU cc_start: 0.7812 (mp0) cc_final: 0.7393 (mp0) REVERT: B 124 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8114 (tttt) REVERT: B 136 GLN cc_start: 0.7898 (mt0) cc_final: 0.7545 (mt0) REVERT: B 163 ASP cc_start: 0.8160 (p0) cc_final: 0.7839 (p0) REVERT: B 167 ASN cc_start: 0.7652 (m-40) cc_final: 0.7338 (m110) REVERT: B 247 GLN cc_start: 0.8149 (mt0) cc_final: 0.7781 (tt0) REVERT: B 267 PHE cc_start: 0.8710 (m-80) cc_final: 0.8499 (m-80) REVERT: B 300 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7478 (m-40) REVERT: B 325 MET cc_start: 0.8770 (tpp) cc_final: 0.8260 (mmm) REVERT: B 372 LYS cc_start: 0.8379 (ttpp) cc_final: 0.7877 (ttpp) REVERT: B 398 MET cc_start: 0.7424 (mtp) cc_final: 0.7035 (mtt) outliers start: 31 outliers final: 22 residues processed: 152 average time/residue: 0.1831 time to fit residues: 37.8815 Evaluate side-chains 155 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 40.0000 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 0.0970 chunk 43 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 overall best weight: 4.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6990 Z= 0.202 Angle : 0.563 7.574 9512 Z= 0.276 Chirality : 0.045 0.225 1042 Planarity : 0.004 0.060 1231 Dihedral : 12.360 173.845 1084 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.45 % Allowed : 16.83 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.30 (0.28), residues: 850 helix: -1.22 (0.27), residues: 336 sheet: -1.98 (0.43), residues: 137 loop : -1.47 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 388 HIS 0.005 0.001 HIS A 88 PHE 0.021 0.001 PHE B 395 TYR 0.015 0.001 TYR B 312 ARG 0.004 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 0.712 Fit side-chains REVERT: A 176 GLN cc_start: 0.8200 (mm110) cc_final: 0.7960 (mm110) REVERT: A 217 LEU cc_start: 0.8516 (tp) cc_final: 0.8277 (tp) REVERT: A 245 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6703 (p0) REVERT: A 280 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6715 (tptt) REVERT: A 313 MET cc_start: 0.7126 (mtt) cc_final: 0.6876 (mtp) REVERT: A 372 GLN cc_start: 0.7611 (mt0) cc_final: 0.6845 (mp10) REVERT: A 413 MET cc_start: 0.7298 (tpt) cc_final: 0.6168 (mtp) REVERT: A 415 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6602 (tm-30) REVERT: B 6 HIS cc_start: 0.7452 (t70) cc_final: 0.7184 (t-170) REVERT: B 26 ASP cc_start: 0.8051 (m-30) cc_final: 0.7709 (m-30) REVERT: B 110 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7338 (tt0) REVERT: B 113 GLU cc_start: 0.7890 (mp0) cc_final: 0.7470 (mp0) REVERT: B 124 LYS cc_start: 0.8257 (ttmt) cc_final: 0.8019 (tttt) REVERT: B 136 GLN cc_start: 0.7910 (mt0) cc_final: 0.7540 (mt0) REVERT: B 163 ASP cc_start: 0.8166 (p0) cc_final: 0.7835 (p0) REVERT: B 167 ASN cc_start: 0.7661 (m-40) cc_final: 0.7317 (m110) REVERT: B 247 GLN cc_start: 0.8095 (mt0) cc_final: 0.7749 (tt0) REVERT: B 267 PHE cc_start: 0.8728 (m-80) cc_final: 0.8501 (m-80) REVERT: B 325 MET cc_start: 0.8653 (tpp) cc_final: 0.8112 (mmm) REVERT: B 372 LYS cc_start: 0.8373 (ttpp) cc_final: 0.7822 (ttpp) REVERT: B 398 MET cc_start: 0.7492 (mtp) cc_final: 0.7030 (mtt) outliers start: 25 outliers final: 21 residues processed: 150 average time/residue: 0.1954 time to fit residues: 38.6925 Evaluate side-chains 156 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6990 Z= 0.267 Angle : 0.606 7.503 9512 Z= 0.300 Chirality : 0.046 0.232 1042 Planarity : 0.005 0.059 1231 Dihedral : 12.420 172.791 1084 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.86 % Allowed : 16.00 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.28 (0.28), residues: 850 helix: -1.18 (0.27), residues: 336 sheet: -1.99 (0.44), residues: 135 loop : -1.48 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 388 HIS 0.005 0.001 HIS A 88 PHE 0.020 0.002 PHE B 395 TYR 0.018 0.002 TYR B 312 ARG 0.007 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 0.988 Fit side-chains REVERT: A 155 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8463 (mm-30) REVERT: A 176 GLN cc_start: 0.8195 (mm110) cc_final: 0.7945 (mm110) REVERT: A 217 LEU cc_start: 0.8559 (tp) cc_final: 0.8314 (tp) REVERT: A 245 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6598 (p0) REVERT: A 280 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6666 (tptt) REVERT: A 302 MET cc_start: 0.8374 (mmp) cc_final: 0.7685 (mmm) REVERT: A 313 MET cc_start: 0.7066 (mtt) cc_final: 0.6824 (mtp) REVERT: A 372 GLN cc_start: 0.7471 (mt0) cc_final: 0.6671 (mp10) REVERT: A 413 MET cc_start: 0.7408 (tpt) cc_final: 0.6015 (mtp) REVERT: A 415 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6864 (tm-30) REVERT: B 6 HIS cc_start: 0.7683 (t70) cc_final: 0.7026 (t-170) REVERT: B 26 ASP cc_start: 0.8140 (m-30) cc_final: 0.7792 (m-30) REVERT: B 110 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7275 (tt0) REVERT: B 113 GLU cc_start: 0.7897 (mp0) cc_final: 0.7482 (mp0) REVERT: B 124 LYS cc_start: 0.8302 (ttmt) cc_final: 0.8059 (tttt) REVERT: B 136 GLN cc_start: 0.7931 (mt0) cc_final: 0.7637 (mt0) REVERT: B 163 ASP cc_start: 0.8159 (p0) cc_final: 0.7878 (p0) REVERT: B 247 GLN cc_start: 0.8121 (mt0) cc_final: 0.7747 (tt0) REVERT: B 372 LYS cc_start: 0.8387 (ttpp) cc_final: 0.7829 (ttpp) REVERT: B 398 MET cc_start: 0.7465 (mtp) cc_final: 0.6958 (mtt) outliers start: 28 outliers final: 22 residues processed: 146 average time/residue: 0.1930 time to fit residues: 37.4732 Evaluate side-chains 148 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 7 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6990 Z= 0.175 Angle : 0.564 7.240 9512 Z= 0.272 Chirality : 0.045 0.225 1042 Planarity : 0.004 0.058 1231 Dihedral : 11.976 175.163 1084 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.03 % Allowed : 16.97 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.15 (0.29), residues: 850 helix: -0.98 (0.28), residues: 344 sheet: -1.75 (0.45), residues: 137 loop : -1.58 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.005 0.001 HIS A 88 PHE 0.023 0.001 PHE B 395 TYR 0.014 0.001 TYR A 172 ARG 0.010 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.831 Fit side-chains REVERT: A 124 LYS cc_start: 0.8601 (tmtt) cc_final: 0.8112 (tmtt) REVERT: A 155 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8224 (mm-30) REVERT: A 176 GLN cc_start: 0.8179 (mm110) cc_final: 0.7926 (mm110) REVERT: A 217 LEU cc_start: 0.8495 (tp) cc_final: 0.8269 (tp) REVERT: A 302 MET cc_start: 0.8278 (mmp) cc_final: 0.7578 (mmm) REVERT: A 313 MET cc_start: 0.7048 (mtt) cc_final: 0.6794 (mtp) REVERT: A 372 GLN cc_start: 0.7462 (mt0) cc_final: 0.6696 (mp10) REVERT: A 413 MET cc_start: 0.7296 (tpt) cc_final: 0.5947 (mtp) REVERT: A 415 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6573 (tm-30) REVERT: B 6 HIS cc_start: 0.7316 (t70) cc_final: 0.6856 (t-170) REVERT: B 26 ASP cc_start: 0.8131 (m-30) cc_final: 0.7788 (m-30) REVERT: B 110 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7321 (tt0) REVERT: B 113 GLU cc_start: 0.7869 (mp0) cc_final: 0.7640 (mp0) REVERT: B 124 LYS cc_start: 0.8254 (ttmt) cc_final: 0.8013 (tttt) REVERT: B 136 GLN cc_start: 0.7891 (mt0) cc_final: 0.7520 (mt0) REVERT: B 163 ASP cc_start: 0.8189 (p0) cc_final: 0.7856 (p0) REVERT: B 167 ASN cc_start: 0.7659 (m-40) cc_final: 0.7299 (m110) REVERT: B 247 GLN cc_start: 0.8081 (mt0) cc_final: 0.7718 (tt0) REVERT: B 269 MET cc_start: 0.8025 (ptp) cc_final: 0.7638 (ptp) REVERT: B 372 LYS cc_start: 0.8388 (ttpp) cc_final: 0.7810 (ttpp) REVERT: B 398 MET cc_start: 0.7421 (mtp) cc_final: 0.6969 (mtt) outliers start: 22 outliers final: 19 residues processed: 146 average time/residue: 0.2048 time to fit residues: 39.1283 Evaluate side-chains 147 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 30.0000 chunk 78 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 68 optimal weight: 0.4980 chunk 72 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6990 Z= 0.245 Angle : 0.602 7.557 9512 Z= 0.294 Chirality : 0.046 0.239 1042 Planarity : 0.004 0.060 1231 Dihedral : 11.912 174.153 1084 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.17 % Allowed : 17.24 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.11 (0.29), residues: 850 helix: -0.93 (0.28), residues: 339 sheet: -1.90 (0.44), residues: 137 loop : -1.49 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 388 HIS 0.005 0.001 HIS A 88 PHE 0.022 0.002 PHE B 395 TYR 0.016 0.002 TYR A 172 ARG 0.011 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.846 Fit side-chains REVERT: A 124 LYS cc_start: 0.8631 (tmtt) cc_final: 0.8146 (tmtt) REVERT: A 176 GLN cc_start: 0.8172 (mm110) cc_final: 0.7912 (mm110) REVERT: A 217 LEU cc_start: 0.8527 (tp) cc_final: 0.8307 (tp) REVERT: A 302 MET cc_start: 0.8371 (mmp) cc_final: 0.7684 (mmm) REVERT: A 313 MET cc_start: 0.7297 (mtt) cc_final: 0.7071 (mtp) REVERT: A 413 MET cc_start: 0.7326 (tpt) cc_final: 0.5861 (mtp) REVERT: A 415 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6864 (tm-30) REVERT: B 6 HIS cc_start: 0.7605 (t70) cc_final: 0.7002 (t-170) REVERT: B 26 ASP cc_start: 0.8191 (m-30) cc_final: 0.7844 (m-30) REVERT: B 110 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7260 (tt0) REVERT: B 113 GLU cc_start: 0.7870 (mp0) cc_final: 0.7636 (mp0) REVERT: B 124 LYS cc_start: 0.8272 (ttmt) cc_final: 0.8040 (tttt) REVERT: B 136 GLN cc_start: 0.7929 (mt0) cc_final: 0.7571 (mt0) REVERT: B 163 ASP cc_start: 0.8073 (p0) cc_final: 0.7780 (p0) REVERT: B 167 ASN cc_start: 0.7897 (m-40) cc_final: 0.7534 (m110) REVERT: B 247 GLN cc_start: 0.8118 (mt0) cc_final: 0.7733 (tt0) REVERT: B 372 LYS cc_start: 0.8382 (ttpp) cc_final: 0.7781 (ttpp) REVERT: B 398 MET cc_start: 0.7414 (mtp) cc_final: 0.6932 (mtt) outliers start: 23 outliers final: 22 residues processed: 135 average time/residue: 0.1961 time to fit residues: 35.5145 Evaluate side-chains 142 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 30.0000 chunk 53 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6990 Z= 0.267 Angle : 0.623 8.139 9512 Z= 0.304 Chirality : 0.047 0.239 1042 Planarity : 0.005 0.060 1231 Dihedral : 11.872 174.425 1084 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.59 % Allowed : 17.10 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.15 (0.29), residues: 850 helix: -0.98 (0.28), residues: 341 sheet: -1.95 (0.45), residues: 133 loop : -1.50 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 388 HIS 0.005 0.001 HIS A 88 PHE 0.021 0.002 PHE B 395 TYR 0.020 0.002 TYR A 172 ARG 0.010 0.001 ARG B 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 0.903 Fit side-chains REVERT: A 124 LYS cc_start: 0.8640 (tmtt) cc_final: 0.8155 (tmtt) REVERT: A 155 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8265 (mm-30) REVERT: A 176 GLN cc_start: 0.8144 (mm110) cc_final: 0.7935 (mm110) REVERT: A 217 LEU cc_start: 0.8531 (tp) cc_final: 0.8306 (tp) REVERT: A 245 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6603 (p0) REVERT: A 302 MET cc_start: 0.8416 (mmp) cc_final: 0.7760 (mmm) REVERT: A 313 MET cc_start: 0.7325 (mtt) cc_final: 0.7109 (mtp) REVERT: A 415 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6918 (tm-30) REVERT: B 6 HIS cc_start: 0.7603 (t70) cc_final: 0.7006 (t-170) REVERT: B 26 ASP cc_start: 0.8238 (m-30) cc_final: 0.7890 (m-30) REVERT: B 110 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7253 (tt0) REVERT: B 113 GLU cc_start: 0.7829 (mp0) cc_final: 0.7579 (mp0) REVERT: B 124 LYS cc_start: 0.8289 (ttmt) cc_final: 0.8059 (tttt) REVERT: B 136 GLN cc_start: 0.7942 (mt0) cc_final: 0.7622 (mt0) REVERT: B 163 ASP cc_start: 0.8262 (p0) cc_final: 0.7968 (p0) REVERT: B 247 GLN cc_start: 0.8232 (mt0) cc_final: 0.7800 (tt0) REVERT: B 372 LYS cc_start: 0.8417 (ttpp) cc_final: 0.7808 (ttpp) REVERT: B 390 ARG cc_start: 0.8147 (mtp-110) cc_final: 0.7594 (ttm-80) REVERT: B 398 MET cc_start: 0.7411 (mtp) cc_final: 0.6931 (mtt) outliers start: 26 outliers final: 23 residues processed: 140 average time/residue: 0.1913 time to fit residues: 35.6746 Evaluate side-chains 142 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 18 optimal weight: 0.0470 chunk 67 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.126788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.106414 restraints weight = 12163.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.110353 restraints weight = 6199.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.113067 restraints weight = 3968.097| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6990 Z= 0.173 Angle : 0.581 8.406 9512 Z= 0.279 Chirality : 0.045 0.227 1042 Planarity : 0.005 0.064 1231 Dihedral : 11.541 176.996 1084 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.76 % Allowed : 18.07 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.95 (0.29), residues: 850 helix: -0.76 (0.29), residues: 343 sheet: -1.70 (0.46), residues: 135 loop : -1.50 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.005 0.001 HIS A 88 PHE 0.022 0.001 PHE B 395 TYR 0.015 0.001 TYR A 172 ARG 0.016 0.001 ARG B 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1583.85 seconds wall clock time: 29 minutes 57.15 seconds (1797.15 seconds total)