Starting phenix.real_space_refine on Thu Mar 14 13:23:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq1_31254/03_2024/7eq1_31254.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq1_31254/03_2024/7eq1_31254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq1_31254/03_2024/7eq1_31254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq1_31254/03_2024/7eq1_31254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq1_31254/03_2024/7eq1_31254.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq1_31254/03_2024/7eq1_31254.pdb" } resolution = 3.3 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5728 2.51 5 N 1546 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 333": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8999 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1959 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2212 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "S" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1787 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.32, per 1000 atoms: 0.59 Number of scatterers: 8999 At special positions: 0 Unit cell: (115.56, 117.72, 105.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1669 8.00 N 1546 7.00 C 5728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 314 " - pdb=" SG CYS R 404 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 35.0% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 6 through 40 removed outlier: 3.574A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.543A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.654A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.673A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.200A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.996A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.642A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 389 removed outlier: 3.935A pdb=" N ILE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'R' and resid 228 through 233 removed outlier: 3.625A pdb=" N VAL R 231 " --> pdb=" O TYR R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 273 removed outlier: 3.645A pdb=" N CYS R 256 " --> pdb=" O SER R 252 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU R 264 " --> pdb=" O ILE R 260 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE R 271 " --> pdb=" O VAL R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 299 removed outlier: 3.722A pdb=" N LEU R 299 " --> pdb=" O ASN R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 304 removed outlier: 4.104A pdb=" N ALA R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 344 removed outlier: 4.228A pdb=" N ALA R 316 " --> pdb=" O SER R 312 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 353 through 364 removed outlier: 3.570A pdb=" N LEU R 361 " --> pdb=" O LYS R 357 " (cutoff:3.500A) Processing helix chain 'R' and resid 370 through 376 removed outlier: 4.107A pdb=" N SER R 375 " --> pdb=" O LEU R 371 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL R 376 " --> pdb=" O LEU R 372 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 442 removed outlier: 3.581A pdb=" N LEU R 425 " --> pdb=" O GLY R 421 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE R 426 " --> pdb=" O LEU R 422 " (cutoff:3.500A) Processing helix chain 'R' and resid 456 through 467 Processing helix chain 'R' and resid 468 through 473 removed outlier: 3.539A pdb=" N ALA R 473 " --> pdb=" O TRP R 470 " (cutoff:3.500A) Processing helix chain 'R' and resid 480 through 493 removed outlier: 3.640A pdb=" N GLN R 484 " --> pdb=" O PHE R 480 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE R 488 " --> pdb=" O GLN R 484 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR R 489 " --> pdb=" O LEU R 485 " (cutoff:3.500A) Processing helix chain 'R' and resid 494 through 520 Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.612A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.505A pdb=" N ASP S 223 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 220 through 224' Processing helix chain 'Y' and resid 7 through 24 removed outlier: 3.687A pdb=" N GLN Y 11 " --> pdb=" O ALA Y 7 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU Y 15 " --> pdb=" O GLN Y 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.820A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.900A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.900A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.869A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AA6, first strand: chain 'S' and resid 147 through 148 removed outlier: 3.738A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.720A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.696A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.065A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.582A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.928A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.221A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.716A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1167 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: 2.71 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2917 1.34 - 1.46: 2146 1.46 - 1.58: 4053 1.58 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 9197 Sorted by residual: bond pdb=" CB MET S 230 " pdb=" CG MET S 230 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.31e-01 bond pdb=" CG MET B 61 " pdb=" SD MET B 61 " ideal model delta sigma weight residual 1.803 1.782 0.021 2.50e-02 1.60e+03 6.85e-01 bond pdb=" CB PRO S 236 " pdb=" CG PRO S 236 " ideal model delta sigma weight residual 1.506 1.475 0.031 3.90e-02 6.57e+02 6.50e-01 bond pdb=" CB ILE S 58 " pdb=" CG2 ILE S 58 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.25e-01 bond pdb=" CB ARG S 98 " pdb=" CG ARG S 98 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.24e-01 ... (remaining 9192 not shown) Histogram of bond angle deviations from ideal: 96.85 - 104.29: 102 104.29 - 111.74: 4351 111.74 - 119.18: 3111 119.18 - 126.62: 4762 126.62 - 134.07: 149 Bond angle restraints: 12475 Sorted by residual: angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.93e+01 angle pdb=" CA CYS R 404 " pdb=" CB CYS R 404 " pdb=" SG CYS R 404 " ideal model delta sigma weight residual 114.40 120.30 -5.90 2.30e+00 1.89e-01 6.58e+00 angle pdb=" C VAL A 367 " pdb=" N ASP A 368 " pdb=" CA ASP A 368 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.45e+00 angle pdb=" C PRO R 241 " pdb=" N ALA R 242 " pdb=" CA ALA R 242 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.98e+00 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.49e+00 ... (remaining 12470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4922 17.97 - 35.94: 420 35.94 - 53.91: 71 53.91 - 71.88: 10 71.88 - 89.84: 9 Dihedral angle restraints: 5432 sinusoidal: 2100 harmonic: 3332 Sorted by residual: dihedral pdb=" CB CYS R 314 " pdb=" SG CYS R 314 " pdb=" SG CYS R 404 " pdb=" CB CYS R 404 " ideal model delta sinusoidal sigma weight residual -86.00 -158.88 72.88 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CA LEU R 235 " pdb=" C LEU R 235 " pdb=" N SER R 236 " pdb=" CA SER R 236 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA VAL B 213 " pdb=" C VAL B 213 " pdb=" N ARG B 214 " pdb=" CA ARG B 214 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 831 0.031 - 0.062: 391 0.062 - 0.093: 125 0.093 - 0.124: 54 0.124 - 0.155: 10 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CB ILE R 386 " pdb=" CA ILE R 386 " pdb=" CG1 ILE R 386 " pdb=" CG2 ILE R 386 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CB THR S 91 " pdb=" CA THR S 91 " pdb=" OG1 THR S 91 " pdb=" CG2 THR S 91 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA VAL R 240 " pdb=" N VAL R 240 " pdb=" C VAL R 240 " pdb=" CB VAL R 240 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1408 not shown) Planarity restraints: 1581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.015 2.00e-02 2.50e+03 1.22e-02 2.97e+00 pdb=" CG TYR B 59 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE S 239 " 0.012 2.00e-02 2.50e+03 1.25e-02 2.75e+00 pdb=" CG PHE S 239 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE S 239 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE S 239 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE S 239 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE S 239 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE S 239 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 309 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO R 310 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO R 310 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 310 " -0.021 5.00e-02 4.00e+02 ... (remaining 1578 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 156 2.67 - 3.23: 8576 3.23 - 3.78: 14129 3.78 - 4.34: 19172 4.34 - 4.90: 31434 Nonbonded interactions: 73467 Sorted by model distance: nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.113 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.129 2.440 nonbonded pdb=" OD2 ASP Y 48 " pdb=" OG SER B 281 " model vdw 2.144 2.440 nonbonded pdb=" O PHE A 376 " pdb=" OH TYR R 347 " model vdw 2.180 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.202 2.440 ... (remaining 73462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.150 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.350 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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 : 0.003 0.037 9197 Z= 0.210 Angle : 0.584 8.383 12475 Z= 0.310 Chirality : 0.042 0.155 1411 Planarity : 0.004 0.040 1581 Dihedral : 13.831 89.845 3278 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 1134 helix: 0.75 (0.29), residues: 363 sheet: -0.43 (0.30), residues: 282 loop : -1.18 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.028 0.002 PHE S 239 TYR 0.030 0.002 TYR B 59 ARG 0.006 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.042 Fit side-chains REVERT: A 9 ASP cc_start: 0.7432 (m-30) cc_final: 0.7182 (m-30) REVERT: A 207 ILE cc_start: 0.8337 (mm) cc_final: 0.8119 (mm) REVERT: A 327 GLU cc_start: 0.7680 (mp0) cc_final: 0.7364 (mp0) REVERT: R 361 LEU cc_start: 0.8508 (tp) cc_final: 0.8182 (tp) REVERT: R 485 LEU cc_start: 0.7710 (mt) cc_final: 0.7486 (mm) REVERT: R 492 ASN cc_start: 0.8280 (m-40) cc_final: 0.7836 (m-40) REVERT: S 192 MET cc_start: 0.7267 (ptt) cc_final: 0.7067 (ptt) REVERT: B 27 ASP cc_start: 0.7392 (p0) cc_final: 0.7073 (p0) REVERT: B 37 ILE cc_start: 0.8616 (mm) cc_final: 0.8406 (mm) REVERT: B 44 GLN cc_start: 0.6858 (mp-120) cc_final: 0.5873 (mp-120) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2475 time to fit residues: 64.3650 Evaluate side-chains 184 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN R 454 HIS B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9197 Z= 0.204 Angle : 0.557 7.024 12475 Z= 0.289 Chirality : 0.042 0.173 1411 Planarity : 0.004 0.036 1581 Dihedral : 4.528 20.731 1251 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.54 % Allowed : 10.05 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.26), residues: 1134 helix: 0.78 (0.29), residues: 373 sheet: -0.22 (0.30), residues: 284 loop : -1.21 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.026 0.002 PHE S 68 TYR 0.015 0.001 TYR A 391 ARG 0.007 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7467 (m-30) cc_final: 0.7235 (m-30) REVERT: A 207 ILE cc_start: 0.8390 (mm) cc_final: 0.8114 (mm) REVERT: A 216 LYS cc_start: 0.8254 (mppt) cc_final: 0.7895 (mppt) REVERT: A 293 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7743 (mtmm) REVERT: A 327 GLU cc_start: 0.7594 (mp0) cc_final: 0.7272 (mp0) REVERT: A 356 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6802 (mtp180) REVERT: R 492 ASN cc_start: 0.8311 (m-40) cc_final: 0.7892 (m-40) REVERT: S 174 LEU cc_start: 0.8112 (tp) cc_final: 0.7852 (tp) REVERT: B 27 ASP cc_start: 0.7347 (p0) cc_final: 0.7091 (p0) REVERT: B 37 ILE cc_start: 0.8648 (mm) cc_final: 0.8411 (mm) REVERT: B 42 ARG cc_start: 0.6531 (ttt-90) cc_final: 0.6233 (ttt-90) REVERT: B 44 GLN cc_start: 0.6869 (mp-120) cc_final: 0.6354 (mp-120) REVERT: B 61 MET cc_start: 0.7458 (ptm) cc_final: 0.7238 (ptm) REVERT: B 223 THR cc_start: 0.7533 (t) cc_final: 0.7262 (p) REVERT: B 275 SER cc_start: 0.7560 (t) cc_final: 0.7349 (t) outliers start: 15 outliers final: 11 residues processed: 197 average time/residue: 0.2385 time to fit residues: 62.2860 Evaluate side-chains 194 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 182 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 464 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 0.0070 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9197 Z= 0.162 Angle : 0.517 6.681 12475 Z= 0.268 Chirality : 0.041 0.157 1411 Planarity : 0.003 0.037 1581 Dihedral : 4.315 19.648 1251 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.05 % Allowed : 13.13 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1134 helix: 1.33 (0.29), residues: 352 sheet: -0.12 (0.30), residues: 284 loop : -1.17 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.001 PHE S 68 TYR 0.013 0.001 TYR A 391 ARG 0.003 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7508 (m-30) cc_final: 0.7252 (m-30) REVERT: A 216 LYS cc_start: 0.8195 (mppt) cc_final: 0.7873 (mppt) REVERT: A 293 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7800 (mtmm) REVERT: A 327 GLU cc_start: 0.7577 (mp0) cc_final: 0.7261 (mp0) REVERT: A 356 ARG cc_start: 0.6981 (mpp-170) cc_final: 0.6763 (mtp180) REVERT: R 295 ASN cc_start: 0.6363 (m110) cc_final: 0.6059 (m110) REVERT: R 492 ASN cc_start: 0.8278 (m-40) cc_final: 0.7912 (m-40) REVERT: S 32 PHE cc_start: 0.7653 (m-80) cc_final: 0.7383 (m-10) REVERT: S 139 VAL cc_start: 0.8125 (m) cc_final: 0.7909 (t) REVERT: S 174 LEU cc_start: 0.8076 (tp) cc_final: 0.7710 (tp) REVERT: B 27 ASP cc_start: 0.7272 (p0) cc_final: 0.7030 (p0) REVERT: B 37 ILE cc_start: 0.8625 (mm) cc_final: 0.8382 (mm) REVERT: B 52 ARG cc_start: 0.7570 (mtm-85) cc_final: 0.7334 (mtt-85) REVERT: B 61 MET cc_start: 0.7501 (ptm) cc_final: 0.7131 (ptm) REVERT: B 186 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6681 (p0) REVERT: B 197 ARG cc_start: 0.6841 (ttm-80) cc_final: 0.6627 (ttm-80) REVERT: B 223 THR cc_start: 0.7514 (t) cc_final: 0.7267 (p) REVERT: B 275 SER cc_start: 0.7566 (t) cc_final: 0.7343 (t) REVERT: B 317 CYS cc_start: 0.6880 (p) cc_final: 0.6551 (p) outliers start: 20 outliers final: 13 residues processed: 200 average time/residue: 0.2494 time to fit residues: 66.8923 Evaluate side-chains 199 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9197 Z= 0.215 Angle : 0.542 7.662 12475 Z= 0.279 Chirality : 0.042 0.158 1411 Planarity : 0.003 0.037 1581 Dihedral : 4.400 19.955 1251 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.97 % Allowed : 14.67 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1134 helix: 1.29 (0.29), residues: 357 sheet: -0.15 (0.30), residues: 284 loop : -1.12 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 362 PHE 0.023 0.001 PHE S 68 TYR 0.015 0.001 TYR A 391 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 0.972 Fit side-chains REVERT: A 216 LYS cc_start: 0.8182 (mppt) cc_final: 0.7871 (mppt) REVERT: A 222 PHE cc_start: 0.7921 (m-80) cc_final: 0.7717 (m-80) REVERT: A 293 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7989 (mtpp) REVERT: A 327 GLU cc_start: 0.7591 (mp0) cc_final: 0.7253 (mp0) REVERT: A 345 PHE cc_start: 0.7780 (m-80) cc_final: 0.7417 (m-80) REVERT: A 356 ARG cc_start: 0.6936 (mpp-170) cc_final: 0.6729 (mtp180) REVERT: R 492 ASN cc_start: 0.8287 (m-40) cc_final: 0.7977 (m-40) REVERT: S 174 LEU cc_start: 0.8215 (tp) cc_final: 0.7954 (tp) REVERT: B 27 ASP cc_start: 0.7279 (p0) cc_final: 0.7014 (p0) REVERT: B 32 GLN cc_start: 0.7764 (mt0) cc_final: 0.7469 (mt0) REVERT: B 37 ILE cc_start: 0.8639 (mm) cc_final: 0.8419 (mm) REVERT: B 42 ARG cc_start: 0.6619 (ttt-90) cc_final: 0.6239 (ttt-90) REVERT: B 44 GLN cc_start: 0.6888 (mp-120) cc_final: 0.5802 (mp-120) REVERT: B 52 ARG cc_start: 0.7614 (mtm-85) cc_final: 0.7370 (mtt-85) REVERT: B 61 MET cc_start: 0.7533 (ptm) cc_final: 0.7146 (ptm) REVERT: B 186 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6744 (p0) REVERT: B 223 THR cc_start: 0.7617 (t) cc_final: 0.7359 (p) REVERT: B 234 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: B 275 SER cc_start: 0.7591 (t) cc_final: 0.7360 (t) REVERT: B 317 CYS cc_start: 0.6908 (p) cc_final: 0.6574 (p) outliers start: 29 outliers final: 19 residues processed: 209 average time/residue: 0.2372 time to fit residues: 65.7807 Evaluate side-chains 210 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.0060 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9197 Z= 0.184 Angle : 0.525 7.043 12475 Z= 0.270 Chirality : 0.041 0.173 1411 Planarity : 0.003 0.036 1581 Dihedral : 4.338 19.795 1251 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.87 % Allowed : 16.62 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1134 helix: 1.36 (0.29), residues: 358 sheet: -0.12 (0.30), residues: 284 loop : -1.12 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.026 0.001 PHE S 68 TYR 0.014 0.001 TYR A 391 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 1.085 Fit side-chains REVERT: A 8 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6698 (mt-10) REVERT: A 222 PHE cc_start: 0.7919 (m-80) cc_final: 0.7718 (m-80) REVERT: A 327 GLU cc_start: 0.7579 (mp0) cc_final: 0.7238 (mp0) REVERT: A 345 PHE cc_start: 0.7787 (m-80) cc_final: 0.7450 (m-80) REVERT: R 492 ASN cc_start: 0.8265 (m-40) cc_final: 0.7931 (m-40) REVERT: S 32 PHE cc_start: 0.7757 (m-80) cc_final: 0.7388 (m-80) REVERT: S 139 VAL cc_start: 0.8154 (m) cc_final: 0.7926 (t) REVERT: S 174 LEU cc_start: 0.8175 (tp) cc_final: 0.7911 (tp) REVERT: S 227 TYR cc_start: 0.8131 (m-80) cc_final: 0.7879 (m-80) REVERT: B 32 GLN cc_start: 0.7724 (mt0) cc_final: 0.7437 (mt0) REVERT: B 37 ILE cc_start: 0.8620 (mm) cc_final: 0.8411 (mm) REVERT: B 42 ARG cc_start: 0.6558 (ttt-90) cc_final: 0.6196 (ttt-90) REVERT: B 44 GLN cc_start: 0.6919 (mp-120) cc_final: 0.5708 (mp-120) REVERT: B 52 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.7388 (mtt-85) REVERT: B 59 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.6858 (m-10) REVERT: B 61 MET cc_start: 0.7550 (ptm) cc_final: 0.7135 (ptm) REVERT: B 186 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6747 (p0) REVERT: B 223 THR cc_start: 0.7593 (t) cc_final: 0.7348 (p) REVERT: B 234 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: B 275 SER cc_start: 0.7572 (t) cc_final: 0.7340 (t) REVERT: B 317 CYS cc_start: 0.6919 (p) cc_final: 0.6589 (p) outliers start: 28 outliers final: 17 residues processed: 211 average time/residue: 0.2440 time to fit residues: 68.2885 Evaluate side-chains 216 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS A 371 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9197 Z= 0.225 Angle : 0.545 6.678 12475 Z= 0.280 Chirality : 0.042 0.180 1411 Planarity : 0.003 0.035 1581 Dihedral : 4.412 20.104 1251 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.59 % Allowed : 16.41 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1134 helix: 1.37 (0.29), residues: 357 sheet: -0.33 (0.30), residues: 277 loop : -1.09 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE S 68 TYR 0.016 0.001 TYR A 391 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 1.061 Fit side-chains REVERT: A 8 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6748 (mt-10) REVERT: A 216 LYS cc_start: 0.8186 (mppt) cc_final: 0.7982 (mppt) REVERT: A 222 PHE cc_start: 0.7926 (m-80) cc_final: 0.7691 (m-80) REVERT: A 283 ARG cc_start: 0.7961 (ttp-110) cc_final: 0.7756 (ttp80) REVERT: A 327 GLU cc_start: 0.7579 (mp0) cc_final: 0.7215 (mp0) REVERT: R 492 ASN cc_start: 0.8299 (m-40) cc_final: 0.7930 (m-40) REVERT: S 32 PHE cc_start: 0.7770 (m-80) cc_final: 0.7377 (m-80) REVERT: S 139 VAL cc_start: 0.8148 (m) cc_final: 0.7931 (t) REVERT: S 174 LEU cc_start: 0.8249 (tp) cc_final: 0.8002 (tp) REVERT: B 32 GLN cc_start: 0.7670 (mt0) cc_final: 0.7455 (mt0) REVERT: B 37 ILE cc_start: 0.8638 (mm) cc_final: 0.8434 (mm) REVERT: B 42 ARG cc_start: 0.6586 (ttt-90) cc_final: 0.6240 (ttt-90) REVERT: B 44 GLN cc_start: 0.6955 (mp-120) cc_final: 0.5895 (mp-120) REVERT: B 52 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7401 (mtt-85) REVERT: B 59 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.7018 (m-10) REVERT: B 186 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6763 (p0) REVERT: B 223 THR cc_start: 0.7616 (t) cc_final: 0.7392 (p) REVERT: B 234 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: B 275 SER cc_start: 0.7619 (t) cc_final: 0.7380 (t) REVERT: B 317 CYS cc_start: 0.6910 (p) cc_final: 0.6597 (p) outliers start: 35 outliers final: 24 residues processed: 219 average time/residue: 0.2375 time to fit residues: 69.1437 Evaluate side-chains 227 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 423 THR Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 464 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9197 Z= 0.177 Angle : 0.533 6.720 12475 Z= 0.273 Chirality : 0.041 0.184 1411 Planarity : 0.003 0.035 1581 Dihedral : 4.349 20.118 1251 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.38 % Allowed : 18.36 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1134 helix: 1.40 (0.29), residues: 353 sheet: -0.22 (0.30), residues: 278 loop : -1.10 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.030 0.001 PHE S 68 TYR 0.016 0.001 TYR A 391 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 205 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6701 (mt-10) REVERT: A 216 LYS cc_start: 0.8158 (mppt) cc_final: 0.7949 (mppt) REVERT: A 222 PHE cc_start: 0.7908 (m-80) cc_final: 0.7695 (m-80) REVERT: A 327 GLU cc_start: 0.7559 (mp0) cc_final: 0.7159 (mp0) REVERT: R 492 ASN cc_start: 0.8259 (m-40) cc_final: 0.7921 (m-40) REVERT: S 32 PHE cc_start: 0.7797 (m-80) cc_final: 0.7315 (m-80) REVERT: S 139 VAL cc_start: 0.8162 (m) cc_final: 0.7944 (t) REVERT: S 174 LEU cc_start: 0.8161 (tp) cc_final: 0.7922 (tp) REVERT: S 230 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7158 (tpp) REVERT: B 27 ASP cc_start: 0.7214 (p0) cc_final: 0.6960 (p0) REVERT: B 32 GLN cc_start: 0.7696 (mt0) cc_final: 0.7442 (mt0) REVERT: B 37 ILE cc_start: 0.8614 (mm) cc_final: 0.8400 (mm) REVERT: B 42 ARG cc_start: 0.6573 (ttt-90) cc_final: 0.6219 (ttt-90) REVERT: B 44 GLN cc_start: 0.6945 (mp-120) cc_final: 0.5880 (mp-120) REVERT: B 52 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7378 (mtt-85) REVERT: B 55 LEU cc_start: 0.8149 (mp) cc_final: 0.7906 (mp) REVERT: B 59 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.6993 (m-10) REVERT: B 186 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6752 (p0) REVERT: B 223 THR cc_start: 0.7611 (t) cc_final: 0.7339 (p) REVERT: B 234 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: B 275 SER cc_start: 0.7606 (t) cc_final: 0.7360 (t) outliers start: 33 outliers final: 21 residues processed: 223 average time/residue: 0.2367 time to fit residues: 70.3090 Evaluate side-chains 229 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 423 THR Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS A 371 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9197 Z= 0.269 Angle : 0.575 7.041 12475 Z= 0.297 Chirality : 0.043 0.191 1411 Planarity : 0.004 0.038 1581 Dihedral : 4.543 20.546 1251 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.59 % Allowed : 18.15 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1134 helix: 1.33 (0.29), residues: 353 sheet: -0.30 (0.29), residues: 299 loop : -1.10 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS B 183 PHE 0.028 0.002 PHE S 68 TYR 0.019 0.002 TYR A 391 ARG 0.009 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 207 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: R 492 ASN cc_start: 0.8309 (m-40) cc_final: 0.7976 (m-40) REVERT: S 139 VAL cc_start: 0.8171 (m) cc_final: 0.7954 (t) REVERT: S 174 LEU cc_start: 0.8308 (tp) cc_final: 0.8050 (tp) REVERT: S 224 VAL cc_start: 0.8388 (p) cc_final: 0.8113 (t) REVERT: B 27 ASP cc_start: 0.7221 (p0) cc_final: 0.6940 (p0) REVERT: B 32 GLN cc_start: 0.7742 (mt0) cc_final: 0.7502 (mt0) REVERT: B 42 ARG cc_start: 0.6597 (ttt-90) cc_final: 0.6304 (ttt-90) REVERT: B 44 GLN cc_start: 0.6962 (mp-120) cc_final: 0.6039 (mp-120) REVERT: B 52 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.7418 (mtt-85) REVERT: B 59 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.7120 (m-10) REVERT: B 186 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6765 (p0) REVERT: B 223 THR cc_start: 0.7653 (t) cc_final: 0.7426 (p) REVERT: B 275 SER cc_start: 0.7659 (t) cc_final: 0.7415 (t) REVERT: B 317 CYS cc_start: 0.6783 (p) cc_final: 0.6554 (p) outliers start: 35 outliers final: 24 residues processed: 226 average time/residue: 0.2533 time to fit residues: 75.4404 Evaluate side-chains 231 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 205 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 423 THR Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 464 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9197 Z= 0.209 Angle : 0.566 8.131 12475 Z= 0.290 Chirality : 0.042 0.203 1411 Planarity : 0.004 0.035 1581 Dihedral : 4.499 20.893 1251 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.87 % Allowed : 19.90 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1134 helix: 1.37 (0.29), residues: 353 sheet: -0.24 (0.30), residues: 279 loop : -1.11 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.028 0.001 PHE S 68 TYR 0.016 0.001 TYR A 391 ARG 0.011 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.7931 (m-80) cc_final: 0.7712 (m-80) REVERT: A 246 PHE cc_start: 0.7981 (t80) cc_final: 0.7768 (t80) REVERT: R 492 ASN cc_start: 0.8265 (m-40) cc_final: 0.7931 (m-40) REVERT: S 32 PHE cc_start: 0.7821 (m-80) cc_final: 0.7341 (m-80) REVERT: S 174 LEU cc_start: 0.8176 (tp) cc_final: 0.7938 (tp) REVERT: B 32 GLN cc_start: 0.7729 (mt0) cc_final: 0.7475 (mt0) REVERT: B 42 ARG cc_start: 0.6575 (ttt-90) cc_final: 0.6317 (ttt-90) REVERT: B 44 GLN cc_start: 0.6948 (mp-120) cc_final: 0.6019 (mp-120) REVERT: B 55 LEU cc_start: 0.8110 (mp) cc_final: 0.7868 (mp) REVERT: B 59 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.7023 (m-10) REVERT: B 186 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6745 (p0) REVERT: B 223 THR cc_start: 0.7615 (t) cc_final: 0.7371 (p) REVERT: B 275 SER cc_start: 0.7643 (t) cc_final: 0.7390 (t) REVERT: B 317 CYS cc_start: 0.6798 (p) cc_final: 0.6522 (p) outliers start: 28 outliers final: 20 residues processed: 218 average time/residue: 0.2270 time to fit residues: 66.7180 Evaluate side-chains 228 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 423 THR Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9197 Z= 0.203 Angle : 0.571 6.998 12475 Z= 0.292 Chirality : 0.042 0.206 1411 Planarity : 0.004 0.041 1581 Dihedral : 4.494 20.432 1251 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.67 % Allowed : 20.10 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1134 helix: 1.40 (0.29), residues: 352 sheet: -0.33 (0.30), residues: 270 loop : -1.16 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.028 0.001 PHE S 68 TYR 0.014 0.001 TYR A 391 ARG 0.011 0.000 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.7902 (m-80) cc_final: 0.7687 (m-80) REVERT: A 246 PHE cc_start: 0.7956 (t80) cc_final: 0.7734 (t80) REVERT: R 492 ASN cc_start: 0.8258 (m-40) cc_final: 0.7937 (m-40) REVERT: S 32 PHE cc_start: 0.7814 (m-80) cc_final: 0.7330 (m-80) REVERT: S 174 LEU cc_start: 0.8198 (tp) cc_final: 0.7970 (tp) REVERT: B 22 ARG cc_start: 0.7383 (mtt180) cc_final: 0.7150 (mtt90) REVERT: B 32 GLN cc_start: 0.7726 (mt0) cc_final: 0.7464 (mt0) REVERT: B 42 ARG cc_start: 0.6588 (ttt-90) cc_final: 0.6322 (ttt-90) REVERT: B 44 GLN cc_start: 0.6936 (mp-120) cc_final: 0.6022 (mp-120) REVERT: B 55 LEU cc_start: 0.8112 (mp) cc_final: 0.7875 (mp) REVERT: B 59 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6928 (m-10) REVERT: B 186 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6724 (p0) REVERT: B 223 THR cc_start: 0.7584 (t) cc_final: 0.7359 (p) REVERT: B 275 SER cc_start: 0.7616 (t) cc_final: 0.7360 (t) REVERT: B 317 CYS cc_start: 0.6804 (p) cc_final: 0.6480 (p) outliers start: 26 outliers final: 21 residues processed: 219 average time/residue: 0.2298 time to fit residues: 67.8520 Evaluate side-chains 222 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 199 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 423 THR Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 88 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.133133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115086 restraints weight = 12634.543| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.88 r_work: 0.3307 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9197 Z= 0.174 Angle : 0.559 6.803 12475 Z= 0.286 Chirality : 0.041 0.196 1411 Planarity : 0.004 0.040 1581 Dihedral : 4.408 20.123 1251 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.56 % Allowed : 20.92 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1134 helix: 1.51 (0.29), residues: 347 sheet: -0.31 (0.30), residues: 270 loop : -1.22 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.020 0.001 PHE S 68 TYR 0.012 0.001 TYR R 381 ARG 0.011 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2445.34 seconds wall clock time: 44 minutes 33.26 seconds (2673.26 seconds total)