Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 11:48:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2i_0331/10_2023/6i2i_0331_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2i_0331/10_2023/6i2i_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_0331/10_2023/6i2i_0331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2i_0331/10_2023/6i2i_0331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2i_0331/10_2023/6i2i_0331_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2i_0331/10_2023/6i2i_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-1.21rc1-5097/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: 4.39, per 1000 atoms: 0.64 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: 2.88 Conformation dependent library (CDL) restraints added in 996.6 milliseconds 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: 1.14 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: 1.62 Time building geometry restraints manager: 3.04 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: 4059 33.48 - 66.97: 38 66.97 - 100.45: 6 100.45 - 133.93: 1 133.93 - 167.41: 3 Dihedral angle restraints: 4107 sinusoidal: 1636 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 4104 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: 0.020 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: 0.000 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.580 Find NCS groups from input model: 0.200 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- 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 : 12.379 167.414 2523 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 *********************** 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 : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 220 average time/residue: 0.2143 time to fit residues: 60.8092 Evaluate side-chains 139 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0625 time to fit residues: 1.2302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 329 ASN A 372 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 91 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN B 258 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6990 Z= 0.209 Angle : 0.667 7.935 9512 Z= 0.326 Chirality : 0.045 0.209 1042 Planarity : 0.006 0.061 1231 Dihedral : 12.016 174.503 954 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.76 % Allowed : 12.00 % Favored : 85.24 % 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: -4.00 (0.25), residues: 850 helix: -3.01 (0.21), residues: 337 sheet: -2.60 (0.41), residues: 138 loop : -2.13 (0.29), residues: 375 *********************** 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 182 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 173 average time/residue: 0.2171 time to fit residues: 49.0191 Evaluate side-chains 139 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0687 time to fit residues: 2.7020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 52 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 68 optimal weight: 0.0980 chunk 76 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 overall best weight: 8.6190 ------------------------------------------------------------------------------- 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 ** 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 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN B 406 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6990 Z= 0.353 Angle : 0.719 8.228 9512 Z= 0.359 Chirality : 0.049 0.179 1042 Planarity : 0.006 0.061 1231 Dihedral : 11.876 169.436 954 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.48 % Allowed : 14.21 % Favored : 83.31 % 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: -3.53 (0.26), residues: 850 helix: -2.45 (0.24), residues: 342 sheet: -2.60 (0.42), residues: 131 loop : -1.94 (0.30), residues: 377 *********************** 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 150 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 143 average time/residue: 0.2007 time to fit residues: 38.1176 Evaluate side-chains 126 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0623 time to fit residues: 2.3779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 0.0470 chunk 36 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 197 HIS A 256 GLN A 406 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6990 Z= 0.147 Angle : 0.595 8.285 9512 Z= 0.284 Chirality : 0.044 0.180 1042 Planarity : 0.004 0.057 1231 Dihedral : 11.294 174.587 954 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.10 % Allowed : 16.00 % Favored : 82.90 % 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: -3.04 (0.27), residues: 850 helix: -2.07 (0.25), residues: 344 sheet: -2.22 (0.44), residues: 132 loop : -1.69 (0.31), residues: 374 *********************** 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 144 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.092 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 139 average time/residue: 0.2562 time to fit residues: 48.1645 Evaluate side-chains 123 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0735 time to fit residues: 1.8083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 61 optimal weight: 0.0980 chunk 33 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 0.1980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6990 Z= 0.154 Angle : 0.585 9.191 9512 Z= 0.276 Chirality : 0.044 0.165 1042 Planarity : 0.004 0.058 1231 Dihedral : 11.223 176.612 954 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.66 % Allowed : 16.28 % Favored : 82.07 % 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: -2.53 (0.28), residues: 850 helix: -1.56 (0.26), residues: 338 sheet: -1.95 (0.44), residues: 130 loop : -1.51 (0.32), residues: 382 *********************** 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 144 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.739 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 138 average time/residue: 0.2101 time to fit residues: 38.0684 Evaluate side-chains 125 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0772 time to fit residues: 2.1720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 48 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 overall best weight: 6.5188 ------------------------------------------------------------------------------- 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 ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4463 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= 0.269 Angle : 0.644 8.708 9512 Z= 0.312 Chirality : 0.047 0.192 1042 Planarity : 0.005 0.058 1231 Dihedral : 11.419 173.408 954 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.97 % Allowed : 18.07 % Favored : 80.97 % 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: -2.43 (0.28), residues: 850 helix: -1.39 (0.27), residues: 332 sheet: -2.01 (0.44), residues: 135 loop : -1.49 (0.33), residues: 383 *********************** 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 129 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 0.836 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 126 average time/residue: 0.2598 time to fit residues: 43.8743 Evaluate side-chains 123 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0759 time to fit residues: 2.2440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 51 optimal weight: 0.0470 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- 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 ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** 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: 0.7330 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6990 Z= 0.176 Angle : 0.591 7.873 9512 Z= 0.282 Chirality : 0.045 0.166 1042 Planarity : 0.004 0.059 1231 Dihedral : 11.201 176.120 954 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.83 % Allowed : 17.93 % Favored : 81.24 % 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: -1.23 (0.27), residues: 341 sheet: -1.73 (0.44), residues: 137 loop : -1.53 (0.33), residues: 372 *********************** 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 134 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.818 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 132 average time/residue: 0.1976 time to fit residues: 35.0537 Evaluate side-chains 121 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0775 time to fit residues: 1.5012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 74 optimal weight: 0.0030 chunk 78 optimal weight: 7.9990 overall best weight: 2.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6990 Z= 0.158 Angle : 0.589 7.646 9512 Z= 0.280 Chirality : 0.044 0.159 1042 Planarity : 0.004 0.056 1231 Dihedral : 11.144 178.561 954 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.83 % Allowed : 19.59 % 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: -2.05 (0.29), residues: 850 helix: -1.06 (0.27), residues: 344 sheet: -1.43 (0.46), residues: 137 loop : -1.46 (0.33), residues: 369 *********************** 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 128 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 0.847 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 124 average time/residue: 0.1819 time to fit residues: 30.7814 Evaluate side-chains 115 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0750 time to fit residues: 1.9100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 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 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 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: 0.7343 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6990 Z= 0.230 Angle : 0.632 7.470 9512 Z= 0.304 Chirality : 0.046 0.185 1042 Planarity : 0.004 0.062 1231 Dihedral : 11.236 176.314 954 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.97 % Allowed : 20.00 % Favored : 79.03 % 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: -1.89 (0.29), residues: 850 helix: -0.83 (0.29), residues: 329 sheet: -1.52 (0.46), residues: 137 loop : -1.40 (0.33), residues: 384 *********************** 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 124 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.845 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 122 average time/residue: 0.1971 time to fit residues: 32.3600 Evaluate side-chains 114 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0714 time to fit residues: 1.5190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 71 optimal weight: 0.0570 overall best weight: 4.8106 ------------------------------------------------------------------------------- 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 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6990 Z= 0.223 Angle : 0.642 8.318 9512 Z= 0.306 Chirality : 0.046 0.186 1042 Planarity : 0.005 0.068 1231 Dihedral : 11.147 175.743 954 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.28 % Allowed : 20.14 % 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: -1.91 (0.29), residues: 850 helix: -0.79 (0.29), residues: 328 sheet: -1.63 (0.46), residues: 135 loop : -1.42 (0.33), residues: 387 ********************** 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 116 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.741 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 0.1876 time to fit residues: 29.1457 Evaluate side-chains 112 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0714 time to fit residues: 1.2429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 18 optimal weight: 0.3980 chunk 67 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 overall best weight: 5.2788 ------------------------------------------------------------------------------- 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 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.126961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.106229 restraints weight = 12080.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.110265 restraints weight = 6156.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.113031 restraints weight = 3941.582| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6990 Z= 0.241 Angle : 0.653 8.324 9512 Z= 0.313 Chirality : 0.046 0.186 1042 Planarity : 0.005 0.068 1231 Dihedral : 11.137 175.472 954 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.55 % Allowed : 20.28 % 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: -1.91 (0.29), residues: 850 helix: -0.72 (0.29), residues: 329 sheet: -1.80 (0.45), residues: 139 loop : -1.42 (0.33), residues: 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1554.62 seconds wall clock time: 29 minutes 3.72 seconds (1743.72 seconds total)