Starting phenix.real_space_refine on Thu Jun 27 14:21:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/06_2024/8z9a_39858_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/06_2024/8z9a_39858.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/06_2024/8z9a_39858_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/06_2024/8z9a_39858_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/06_2024/8z9a_39858_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/06_2024/8z9a_39858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/06_2024/8z9a_39858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/06_2024/8z9a_39858_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/06_2024/8z9a_39858_neut_updated.pdb" } resolution = 3.0 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= 0.007 sd= 0.129 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 72 5.16 5 C 8695 2.51 5 N 1981 2.21 5 O 2266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 11": "OD1" <-> "OD2" Residue "A TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "B ASP 6": "OD1" <-> "OD2" Residue "B ASP 11": "OD1" <-> "OD2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "D ASP 5": "OD1" <-> "OD2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 133": "OD1" <-> "OD2" Residue "D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D ASP 290": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 13021 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3292 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 395} Chain breaks: 1 Chain: "B" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3292 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 395} Chain breaks: 1 Chain: "C" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3140 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 379} Chain breaks: 2 Chain: "D" Number of atoms: 2905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2905 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 7, 'TRANS': 349} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'PC1': 1, 'SOU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.53, per 1000 atoms: 0.81 Number of scatterers: 13021 At special positions: 0 Unit cell: (115.56, 129.47, 132.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 7 15.00 O 2266 8.00 N 1981 7.00 C 8695 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: 7.36 Conformation dependent library (CDL) restraints added in 3.4 seconds 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2994 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 2 sheets defined 74.9% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 8 through 11 No H-bonds generated for 'chain 'A' and resid 8 through 11' Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 35 through 64 removed outlier: 3.740A pdb=" N MET A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 94 removed outlier: 3.754A pdb=" N HIS A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 114 through 154 removed outlier: 3.831A pdb=" N ALA A 117 " --> pdb=" O PRO A 114 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP A 149 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 152 " --> pdb=" O TRP A 149 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 153 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 245 removed outlier: 3.525A pdb=" N GLU A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASN A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix removed outlier: 3.700A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 335 Processing helix chain 'A' and resid 338 through 360 removed outlier: 3.787A pdb=" N VAL A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 404 removed outlier: 3.558A pdb=" N ILE A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N MET A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 442 through 462 Processing helix chain 'B' and resid 8 through 11 No H-bonds generated for 'chain 'B' and resid 8 through 11' Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 37 through 65 Processing helix chain 'B' and resid 70 through 94 removed outlier: 3.807A pdb=" N HIS B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 114 through 151 removed outlier: 4.802A pdb=" N GLU B 118 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS B 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA B 125 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG B 132 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 137 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 138 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR B 142 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 144 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 148 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 245 removed outlier: 3.650A pdb=" N MET B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix removed outlier: 3.590A pdb=" N SER B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 335 Processing helix chain 'B' and resid 338 through 360 removed outlier: 3.834A pdb=" N VAL B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 397 removed outlier: 3.961A pdb=" N PHE B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS B 388 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 442 through 462 Processing helix chain 'C' and resid 8 through 11 No H-bonds generated for 'chain 'C' and resid 8 through 11' Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 37 through 65 Processing helix chain 'C' and resid 70 through 94 removed outlier: 3.698A pdb=" N HIS C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 91 " --> pdb=" O MET C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 117 through 148 removed outlier: 4.176A pdb=" N LYS C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 127 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 135 " --> pdb=" O MET C 131 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 245 removed outlier: 3.503A pdb=" N LEU C 210 " --> pdb=" O PHE C 207 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET C 216 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA C 227 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN C 239 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 305 through 335 Processing helix chain 'C' and resid 337 through 359 removed outlier: 3.692A pdb=" N VAL C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 396 removed outlier: 3.903A pdb=" N ILE C 382 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS C 388 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 405 Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 413 through 425 Processing helix chain 'C' and resid 442 through 462 Processing helix chain 'D' and resid 5 through 14 removed outlier: 3.954A pdb=" N MET D 9 " --> pdb=" O ASP D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 45 Processing helix chain 'D' and resid 51 through 76 removed outlier: 3.566A pdb=" N PHE D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 89 Processing helix chain 'D' and resid 95 through 123 Proline residue: D 119 - end of helix Processing helix chain 'D' and resid 150 through 201 removed outlier: 3.925A pdb=" N SER D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 164 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 256 removed outlier: 5.032A pdb=" N LYS D 231 " --> pdb=" O ILE D 227 " (cutoff:3.500A) Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 261 through 286 removed outlier: 4.682A pdb=" N ILE D 268 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER D 270 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER D 271 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA D 273 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D 274 " --> pdb=" O SER D 271 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 275 " --> pdb=" O ALA D 272 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE D 276 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE D 278 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR D 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR D 282 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 283 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR D 284 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY D 285 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.853A pdb=" N ILE D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.515A pdb=" N THR D 323 " --> pdb=" O MET D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 359 removed outlier: 3.930A pdb=" N LEU D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 159 through 163 Processing sheet with id= B, first strand: chain 'B' and resid 159 through 163 871 hydrogen bonds defined for protein. 2286 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: 3.74 Time building geometry restraints manager: 7.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1889 1.31 - 1.44: 3948 1.44 - 1.57: 7391 1.57 - 1.69: 15 1.69 - 1.82: 116 Bond restraints: 13359 Sorted by residual: bond pdb=" CA SER D 271 " pdb=" CB SER D 271 " ideal model delta sigma weight residual 1.536 1.443 0.093 1.53e-02 4.27e+03 3.72e+01 bond pdb=" CA SER D 270 " pdb=" CB SER D 270 " ideal model delta sigma weight residual 1.531 1.438 0.093 1.72e-02 3.38e+03 2.90e+01 bond pdb=" C2 SOU D 402 " pdb=" O2 SOU D 402 " ideal model delta sigma weight residual 1.408 1.324 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C21 PC1 B 502 " pdb=" O21 PC1 B 502 " ideal model delta sigma weight residual 1.331 1.406 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C21 PC1 C 501 " pdb=" O21 PC1 C 501 " ideal model delta sigma weight residual 1.331 1.405 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 13354 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.86: 175 105.86 - 112.91: 7527 112.91 - 119.96: 4444 119.96 - 127.01: 5793 127.01 - 134.06: 145 Bond angle restraints: 18084 Sorted by residual: angle pdb=" C11 SOU D 402 " pdb=" C10 SOU D 402 " pdb=" C12 SOU D 402 " ideal model delta sigma weight residual 68.19 114.36 -46.17 3.00e+00 1.11e-01 2.37e+02 angle pdb=" C11 SOU D 402 " pdb=" C10 SOU D 402 " pdb=" C9 SOU D 402 " ideal model delta sigma weight residual 85.84 122.96 -37.12 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C12 SOU D 402 " pdb=" C10 SOU D 402 " pdb=" C9 SOU D 402 " ideal model delta sigma weight residual 152.68 122.68 30.00 3.00e+00 1.11e-01 1.00e+02 angle pdb=" CA PRO D 119 " pdb=" N PRO D 119 " pdb=" CD PRO D 119 " ideal model delta sigma weight residual 112.00 103.08 8.92 1.40e+00 5.10e-01 4.06e+01 angle pdb=" N ILE D 124 " pdb=" CA ILE D 124 " pdb=" C ILE D 124 " ideal model delta sigma weight residual 112.29 106.85 5.44 9.40e-01 1.13e+00 3.35e+01 ... (remaining 18079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6813 17.71 - 35.42: 726 35.42 - 53.14: 213 53.14 - 70.85: 59 70.85 - 88.56: 11 Dihedral angle restraints: 7822 sinusoidal: 3195 harmonic: 4627 Sorted by residual: dihedral pdb=" CA ASP D 133 " pdb=" C ASP D 133 " pdb=" N PRO D 134 " pdb=" CA PRO D 134 " ideal model delta harmonic sigma weight residual -180.00 -134.40 -45.60 0 5.00e+00 4.00e-02 8.32e+01 dihedral pdb=" CA VAL D 307 " pdb=" C VAL D 307 " pdb=" N SER D 308 " pdb=" CA SER D 308 " ideal model delta harmonic sigma weight residual -180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA SER D 310 " pdb=" C SER D 310 " pdb=" N PHE D 311 " pdb=" CA PHE D 311 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 7819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1357 0.032 - 0.064: 505 0.064 - 0.096: 151 0.096 - 0.127: 42 0.127 - 0.159: 8 Chirality restraints: 2063 Sorted by residual: chirality pdb=" C2 PC1 B 502 " pdb=" C1 PC1 B 502 " pdb=" C3 PC1 B 502 " pdb=" O21 PC1 B 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB ILE C 237 " pdb=" CA ILE C 237 " pdb=" CG1 ILE C 237 " pdb=" CG2 ILE C 237 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" C2 PC1 A 502 " pdb=" C1 PC1 A 502 " pdb=" C3 PC1 A 502 " pdb=" O21 PC1 A 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 2060 not shown) Planarity restraints: 2140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 SOU D 402 " 0.051 2.00e-02 2.50e+03 1.38e-01 2.39e+02 pdb=" C11 SOU D 402 " 0.015 2.00e-02 2.50e+03 pdb=" C12 SOU D 402 " -0.124 2.00e-02 2.50e+03 pdb=" C8 SOU D 402 " -0.165 2.00e-02 2.50e+03 pdb=" C9 SOU D 402 " 0.224 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 SOU D 402 " -0.106 2.00e-02 2.50e+03 8.76e-02 9.59e+01 pdb=" C4 SOU D 402 " 0.137 2.00e-02 2.50e+03 pdb=" C5 SOU D 402 " 0.032 2.00e-02 2.50e+03 pdb=" C6 SOU D 402 " 0.019 2.00e-02 2.50e+03 pdb=" C7 SOU D 402 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 118 " -0.085 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO D 119 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " -0.066 5.00e-02 4.00e+02 ... (remaining 2137 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 346 2.71 - 3.26: 13376 3.26 - 3.81: 21955 3.81 - 4.35: 26985 4.35 - 4.90: 46175 Nonbonded interactions: 108837 Sorted by model distance: nonbonded pdb=" O VAL D 116 " pdb=" OH TYR D 157 " model vdw 2.163 2.440 nonbonded pdb=" OE2 GLU A 320 " pdb=" OH TYR C 409 " model vdw 2.180 2.440 nonbonded pdb=" O PHE D 10 " pdb=" OG1 THR D 14 " model vdw 2.185 2.440 nonbonded pdb=" OH TYR B 409 " pdb=" OE2 GLU C 320 " model vdw 2.197 2.440 nonbonded pdb=" OH TYR C 92 " pdb=" OG SER C 338 " model vdw 2.215 2.440 ... (remaining 108832 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 156 or resid 175 through 463 or resid 501)) selection = (chain 'B' and (resid 5 through 156 or resid 175 through 463 or resid 501)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.030 Extract box with map and model: 3.520 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 50.580 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.005 0.093 13359 Z= 0.358 Angle : 0.980 46.172 18084 Z= 0.399 Chirality : 0.039 0.159 2063 Planarity : 0.006 0.138 2140 Dihedral : 16.723 88.562 4828 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.56 % Allowed : 17.41 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 2.18 (0.22), residues: 1541 helix: 2.10 (0.15), residues: 1209 sheet: 1.55 (1.04), residues: 24 loop : -1.28 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.004 0.001 HIS A 388 PHE 0.020 0.001 PHE B 385 TYR 0.021 0.001 TYR C 44 ARG 0.007 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: D 5 ASP cc_start: 0.7007 (t0) cc_final: 0.6762 (t0) outliers start: 22 outliers final: 19 residues processed: 188 average time/residue: 1.0240 time to fit residues: 213.8261 Evaluate side-chains 175 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 275 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 0.0370 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 322 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.0617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13359 Z= 0.254 Angle : 0.529 22.551 18084 Z= 0.265 Chirality : 0.038 0.158 2063 Planarity : 0.005 0.073 2140 Dihedral : 11.878 95.774 2036 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.68 % Allowed : 14.72 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 2.01 (0.21), residues: 1541 helix: 1.97 (0.15), residues: 1207 sheet: 1.69 (1.08), residues: 24 loop : -1.29 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 408 HIS 0.005 0.001 HIS C 343 PHE 0.022 0.001 PHE B 385 TYR 0.017 0.001 TYR C 44 ARG 0.005 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 174 time to evaluate : 1.250 Fit side-chains REVERT: A 312 ARG cc_start: 0.8032 (ttt180) cc_final: 0.7809 (ttt-90) REVERT: A 320 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8332 (mm-30) REVERT: A 384 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8054 (ttp) REVERT: C 135 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6997 (tp) REVERT: C 136 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6749 (pp) REVERT: C 178 ARG cc_start: 0.6551 (ttm-80) cc_final: 0.6005 (ttt180) REVERT: D 5 ASP cc_start: 0.6966 (t0) cc_final: 0.6646 (t0) REVERT: D 301 ASP cc_start: 0.8706 (t0) cc_final: 0.8493 (t0) outliers start: 52 outliers final: 18 residues processed: 205 average time/residue: 1.0387 time to fit residues: 235.6706 Evaluate side-chains 175 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain D residue 66 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 381 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13359 Z= 0.210 Angle : 0.501 22.396 18084 Z= 0.248 Chirality : 0.037 0.153 2063 Planarity : 0.004 0.065 2140 Dihedral : 11.317 85.774 2018 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.40 % Allowed : 15.92 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 2.07 (0.22), residues: 1541 helix: 2.00 (0.15), residues: 1205 sheet: 1.62 (1.04), residues: 24 loop : -1.16 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.004 0.001 HIS A 212 PHE 0.020 0.001 PHE A 385 TYR 0.020 0.001 TYR C 53 ARG 0.006 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 166 time to evaluate : 1.458 Fit side-chains REVERT: A 312 ARG cc_start: 0.8061 (ttt180) cc_final: 0.7828 (ttt-90) REVERT: A 320 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8285 (mm-30) REVERT: B 42 LYS cc_start: 0.7624 (mtpt) cc_final: 0.7050 (mmtt) REVERT: B 243 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: C 129 SER cc_start: 0.7639 (t) cc_final: 0.7329 (m) REVERT: C 135 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7015 (tp) REVERT: C 136 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7055 (mm) REVERT: C 315 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8550 (mp) REVERT: D 5 ASP cc_start: 0.6950 (t0) cc_final: 0.6618 (t0) REVERT: D 301 ASP cc_start: 0.8581 (t0) cc_final: 0.8294 (t0) outliers start: 48 outliers final: 21 residues processed: 198 average time/residue: 1.0557 time to fit residues: 232.1910 Evaluate side-chains 182 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13359 Z= 0.197 Angle : 0.496 22.249 18084 Z= 0.244 Chirality : 0.037 0.149 2063 Planarity : 0.004 0.062 2140 Dihedral : 11.111 86.871 2018 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.33 % Allowed : 17.27 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.22), residues: 1541 helix: 2.06 (0.15), residues: 1203 sheet: 1.75 (1.03), residues: 24 loop : -1.18 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.004 0.001 HIS A 233 PHE 0.019 0.001 PHE D 115 TYR 0.018 0.001 TYR C 44 ARG 0.006 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 1.484 Fit side-chains REVERT: A 98 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7567 (mmtt) REVERT: A 216 MET cc_start: 0.8579 (mmm) cc_final: 0.8342 (mmm) REVERT: A 320 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8223 (mm-30) REVERT: A 384 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8071 (tpp) REVERT: B 42 LYS cc_start: 0.7622 (mtpt) cc_final: 0.7052 (mmtt) REVERT: C 129 SER cc_start: 0.7643 (t) cc_final: 0.7337 (m) REVERT: C 135 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6962 (tp) REVERT: C 136 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7316 (mm) REVERT: C 137 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6393 (mp) REVERT: C 315 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8562 (mp) REVERT: D 5 ASP cc_start: 0.6972 (t0) cc_final: 0.6636 (t0) REVERT: D 86 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7909 (tp-100) REVERT: D 301 ASP cc_start: 0.8534 (t0) cc_final: 0.8262 (t0) outliers start: 47 outliers final: 18 residues processed: 190 average time/residue: 0.9815 time to fit residues: 207.9252 Evaluate side-chains 176 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 132 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13359 Z= 0.357 Angle : 0.569 22.549 18084 Z= 0.282 Chirality : 0.040 0.156 2063 Planarity : 0.004 0.058 2140 Dihedral : 11.485 87.942 2016 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.75 % Allowed : 17.48 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.22), residues: 1541 helix: 1.78 (0.15), residues: 1209 sheet: 1.65 (1.00), residues: 24 loop : -1.22 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 13 HIS 0.006 0.001 HIS C 343 PHE 0.029 0.001 PHE B 385 TYR 0.022 0.001 TYR C 53 ARG 0.006 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 174 time to evaluate : 1.331 Fit side-chains REVERT: A 312 ARG cc_start: 0.8083 (ttt180) cc_final: 0.7672 (mtp180) REVERT: A 320 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8225 (mm-30) REVERT: A 384 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8135 (ttp) REVERT: B 42 LYS cc_start: 0.7637 (mtpt) cc_final: 0.7103 (mmtt) REVERT: C 129 SER cc_start: 0.7587 (t) cc_final: 0.7334 (m) REVERT: C 135 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6881 (tp) REVERT: C 136 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7311 (mm) REVERT: C 137 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.6116 (mp) REVERT: C 315 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8626 (mp) REVERT: D 5 ASP cc_start: 0.6969 (t0) cc_final: 0.6637 (t0) REVERT: D 301 ASP cc_start: 0.8629 (t0) cc_final: 0.8376 (t0) outliers start: 53 outliers final: 23 residues processed: 205 average time/residue: 1.0377 time to fit residues: 235.5242 Evaluate side-chains 192 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13359 Z= 0.155 Angle : 0.487 22.164 18084 Z= 0.238 Chirality : 0.036 0.138 2063 Planarity : 0.004 0.055 2140 Dihedral : 10.984 89.699 2016 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.19 % Allowed : 19.04 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.22), residues: 1541 helix: 2.09 (0.15), residues: 1203 sheet: 1.82 (1.00), residues: 24 loop : -1.12 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 13 HIS 0.003 0.001 HIS A 233 PHE 0.018 0.001 PHE A 385 TYR 0.018 0.001 TYR C 44 ARG 0.006 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 173 time to evaluate : 1.406 Fit side-chains REVERT: A 98 LYS cc_start: 0.8037 (mptm) cc_final: 0.7454 (mmtt) REVERT: A 312 ARG cc_start: 0.8055 (ttt180) cc_final: 0.7823 (ttt-90) REVERT: A 320 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8221 (mm-30) REVERT: A 395 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: B 42 LYS cc_start: 0.7685 (mtpt) cc_final: 0.7146 (mmtt) REVERT: C 129 SER cc_start: 0.7605 (t) cc_final: 0.7267 (m) REVERT: C 135 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6998 (tp) REVERT: C 137 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6380 (mp) REVERT: C 224 LEU cc_start: 0.7990 (mt) cc_final: 0.7762 (mt) REVERT: C 310 LEU cc_start: 0.7717 (mt) cc_final: 0.7497 (tp) REVERT: D 5 ASP cc_start: 0.6943 (t0) cc_final: 0.6675 (t0) REVERT: D 290 ASP cc_start: 0.7992 (m-30) cc_final: 0.7305 (t0) REVERT: D 301 ASP cc_start: 0.8592 (t0) cc_final: 0.8299 (t0) outliers start: 31 outliers final: 12 residues processed: 194 average time/residue: 1.0229 time to fit residues: 220.8385 Evaluate side-chains 172 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 157 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 43 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 82 optimal weight: 0.0170 chunk 147 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13359 Z= 0.158 Angle : 0.492 22.222 18084 Z= 0.238 Chirality : 0.036 0.209 2063 Planarity : 0.004 0.055 2140 Dihedral : 10.819 89.792 2016 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.76 % Allowed : 19.25 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.22), residues: 1541 helix: 2.19 (0.15), residues: 1196 sheet: 1.81 (1.00), residues: 24 loop : -0.97 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.003 0.001 HIS A 388 PHE 0.016 0.001 PHE A 385 TYR 0.018 0.001 TYR C 53 ARG 0.006 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 170 time to evaluate : 1.367 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8048 (mptm) cc_final: 0.7459 (mmtt) REVERT: A 229 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: A 312 ARG cc_start: 0.8057 (ttt180) cc_final: 0.7819 (ttt-90) REVERT: A 320 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8199 (mm-30) REVERT: A 384 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8108 (tpp) REVERT: A 395 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: B 42 LYS cc_start: 0.7659 (mtpt) cc_final: 0.7106 (mmtt) REVERT: C 129 SER cc_start: 0.7626 (t) cc_final: 0.7238 (m) REVERT: C 135 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6952 (tp) REVERT: C 136 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7104 (pt) REVERT: C 137 ILE cc_start: 0.6575 (OUTLIER) cc_final: 0.6341 (mp) REVERT: C 178 ARG cc_start: 0.6864 (ttt180) cc_final: 0.6459 (ttt180) REVERT: C 310 LEU cc_start: 0.7718 (mt) cc_final: 0.7499 (tp) REVERT: C 315 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8564 (mp) REVERT: D 5 ASP cc_start: 0.6914 (t0) cc_final: 0.6651 (t0) REVERT: D 301 ASP cc_start: 0.8523 (t0) cc_final: 0.8218 (t0) outliers start: 39 outliers final: 16 residues processed: 196 average time/residue: 0.9876 time to fit residues: 215.5564 Evaluate side-chains 185 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13359 Z= 0.167 Angle : 0.498 22.212 18084 Z= 0.240 Chirality : 0.036 0.198 2063 Planarity : 0.004 0.055 2140 Dihedral : 10.596 89.549 2016 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.48 % Allowed : 20.24 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.22), residues: 1541 helix: 2.21 (0.15), residues: 1198 sheet: 1.83 (0.99), residues: 24 loop : -0.95 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.003 0.001 HIS A 233 PHE 0.016 0.001 PHE B 385 TYR 0.019 0.001 TYR D 160 ARG 0.005 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 1.426 Fit side-chains REVERT: A 98 LYS cc_start: 0.8010 (mptm) cc_final: 0.7422 (mmtt) REVERT: A 229 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: A 312 ARG cc_start: 0.8051 (ttt180) cc_final: 0.7557 (mmm160) REVERT: A 320 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8198 (mm-30) REVERT: A 384 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8112 (tpp) REVERT: A 395 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: B 42 LYS cc_start: 0.7665 (mtpt) cc_final: 0.7120 (mmtt) REVERT: C 129 SER cc_start: 0.7612 (t) cc_final: 0.7256 (m) REVERT: C 135 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6984 (tp) REVERT: C 136 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7073 (pt) REVERT: C 137 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6213 (mp) REVERT: C 315 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8564 (mp) REVERT: D 5 ASP cc_start: 0.6907 (t0) cc_final: 0.6633 (t0) REVERT: D 89 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7484 (mtm-85) REVERT: D 301 ASP cc_start: 0.8526 (t0) cc_final: 0.8220 (t0) REVERT: D 347 MET cc_start: 0.5463 (tpp) cc_final: 0.5036 (tpt) outliers start: 35 outliers final: 17 residues processed: 188 average time/residue: 0.9822 time to fit residues: 205.3076 Evaluate side-chains 184 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN D 86 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13359 Z= 0.239 Angle : 0.537 22.316 18084 Z= 0.260 Chirality : 0.038 0.194 2063 Planarity : 0.004 0.055 2140 Dihedral : 10.635 87.200 2015 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.55 % Allowed : 20.24 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.22), residues: 1541 helix: 2.09 (0.15), residues: 1199 sheet: 1.84 (0.99), residues: 24 loop : -1.01 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.005 0.001 HIS A 212 PHE 0.022 0.001 PHE B 385 TYR 0.026 0.001 TYR D 160 ARG 0.006 0.000 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 1.467 Fit side-chains REVERT: A 216 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8279 (mpp) REVERT: A 229 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: A 312 ARG cc_start: 0.8066 (ttt180) cc_final: 0.7566 (mmm160) REVERT: A 320 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8220 (mm-30) REVERT: A 384 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8105 (tpp) REVERT: B 42 LYS cc_start: 0.7634 (mtpt) cc_final: 0.7095 (mmtt) REVERT: C 63 MET cc_start: 0.8162 (ttp) cc_final: 0.7918 (ttp) REVERT: C 129 SER cc_start: 0.7554 (t) cc_final: 0.7289 (m) REVERT: C 135 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6900 (tp) REVERT: C 136 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7107 (pt) REVERT: C 137 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.6138 (mp) REVERT: C 178 ARG cc_start: 0.6974 (ttt180) cc_final: 0.6591 (tpt170) REVERT: C 315 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8586 (mp) REVERT: D 5 ASP cc_start: 0.6943 (t0) cc_final: 0.6673 (t0) REVERT: D 89 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7519 (mtm-85) REVERT: D 301 ASP cc_start: 0.8542 (t0) cc_final: 0.8239 (t0) outliers start: 36 outliers final: 18 residues processed: 185 average time/residue: 0.9878 time to fit residues: 203.3224 Evaluate side-chains 184 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS B 407 HIS D 46 HIS ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13359 Z= 0.176 Angle : 0.515 22.211 18084 Z= 0.249 Chirality : 0.037 0.190 2063 Planarity : 0.004 0.055 2140 Dihedral : 10.399 87.565 2015 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.05 % Allowed : 21.16 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.22), residues: 1541 helix: 2.16 (0.15), residues: 1198 sheet: 1.84 (0.98), residues: 24 loop : -0.95 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.003 0.001 HIS B 233 PHE 0.017 0.001 PHE A 385 TYR 0.029 0.001 TYR D 160 ARG 0.005 0.000 ARG D 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.449 Fit side-chains REVERT: A 216 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8245 (mpp) REVERT: A 229 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: A 312 ARG cc_start: 0.8048 (ttt180) cc_final: 0.7556 (mmm160) REVERT: A 320 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8217 (mm-30) REVERT: A 384 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8124 (tpp) REVERT: B 461 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6294 (tp40) REVERT: C 87 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7291 (mmt) REVERT: C 129 SER cc_start: 0.7547 (t) cc_final: 0.7186 (m) REVERT: C 135 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6961 (tp) REVERT: C 136 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7073 (pt) REVERT: C 137 ILE cc_start: 0.6530 (OUTLIER) cc_final: 0.6273 (mp) REVERT: C 178 ARG cc_start: 0.6859 (ttt180) cc_final: 0.6498 (tpt170) REVERT: D 5 ASP cc_start: 0.6960 (t0) cc_final: 0.6621 (t0) REVERT: D 89 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7463 (mtm-85) REVERT: D 301 ASP cc_start: 0.8540 (t0) cc_final: 0.8237 (t0) outliers start: 29 outliers final: 17 residues processed: 179 average time/residue: 0.9981 time to fit residues: 199.2341 Evaluate side-chains 181 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS B 407 HIS D 86 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106513 restraints weight = 15191.477| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.17 r_work: 0.2909 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13359 Z= 0.165 Angle : 0.518 22.219 18084 Z= 0.249 Chirality : 0.036 0.184 2063 Planarity : 0.004 0.055 2140 Dihedral : 10.321 87.321 2015 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.26 % Allowed : 20.88 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.22), residues: 1541 helix: 2.19 (0.15), residues: 1199 sheet: 1.77 (0.99), residues: 24 loop : -0.92 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.004 0.001 HIS B 407 PHE 0.018 0.001 PHE C 58 TYR 0.031 0.001 TYR D 160 ARG 0.005 0.000 ARG D 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4271.45 seconds wall clock time: 75 minutes 46.23 seconds (4546.23 seconds total)