Starting phenix.real_space_refine on Fri Mar 15 13:59:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ri5_24474/03_2024/7ri5_24474.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ri5_24474/03_2024/7ri5_24474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ri5_24474/03_2024/7ri5_24474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ri5_24474/03_2024/7ri5_24474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ri5_24474/03_2024/7ri5_24474.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ri5_24474/03_2024/7ri5_24474.pdb" } resolution = 4.0 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= 0.000 sd= 0.004 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 32 5.16 5 C 7470 2.51 5 N 2026 2.21 5 O 2338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 464": "OD1" <-> "OD2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 605": "OD1" <-> "OD2" Residue "A TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 622": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 685": "OD1" <-> "OD2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 687": "OD1" <-> "OD2" Residue "A TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 704": "OD1" <-> "OD2" Residue "A PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 746": "OD1" <-> "OD2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 762": "OD1" <-> "OD2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B ASP 101": "OD1" <-> "OD2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B ASP 248": "OD1" <-> "OD2" Residue "B PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B ASP 353": "OD1" <-> "OD2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "C ASP 64": "OD1" <-> "OD2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ASP 131": "OD1" <-> "OD2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 105": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11866 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6183 Classifications: {'peptide': 782} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 750} Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2787 Classifications: {'peptide': 370} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 356} Chain: "C" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 468 Classifications: {'peptide': 65} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 56} Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1752 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "E" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 676 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Time building chain proxies: 6.27, per 1000 atoms: 0.53 Number of scatterers: 11866 At special positions: 0 Unit cell: (102.9, 131.25, 130.2, 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 32 16.00 O 2338 8.00 N 2026 7.00 C 7470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " 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: 3.99 Conformation dependent library (CDL) restraints added in 2.0 seconds 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2780 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 16 sheets defined 24.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.819A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.590A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.042A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 314 Processing helix chain 'A' and resid 361 through 369 removed outlier: 3.648A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'C' and resid 40 through 44 removed outlier: 3.785A pdb=" N ALA C 44 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.683A pdb=" N TYR D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 83 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 122 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.854A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'E' and resid 39 through 46 removed outlier: 4.644A pdb=" N ILE E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 100 removed outlier: 3.770A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER A 150 " --> pdb=" O GLN A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 248 Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 5.000A pdb=" N LEU A 268 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LEU A 337 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY A 270 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL A 339 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 354 removed outlier: 6.596A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 403 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 424 through 430 removed outlier: 3.521A pdb=" N GLN A 441 " --> pdb=" O GLY A 429 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 50 removed outlier: 3.714A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.619A pdb=" N ALA B 66 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA B 83 " --> pdb=" O TRP B 93 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 118 Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 157 removed outlier: 4.823A pdb=" N ALA B 173 " --> pdb=" O TRP B 183 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.793A pdb=" N GLN B 225 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AB4, first strand: chain 'B' and resid 288 through 292 removed outlier: 4.317A pdb=" N ASP B 288 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 328 through 333 removed outlier: 3.778A pdb=" N ASP B 341 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 371 through 374 Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 34 removed outlier: 4.205A pdb=" N THR E 94 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1440 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: 3.50 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3431 1.33 - 1.45: 2350 1.45 - 1.58: 6280 1.58 - 1.70: 1 1.70 - 1.82: 62 Bond restraints: 12124 Sorted by residual: bond pdb=" C ALA B 199 " pdb=" N PRO B 200 " ideal model delta sigma weight residual 1.333 1.295 0.037 1.17e-02 7.31e+03 1.01e+01 bond pdb=" CA THR B 249 " pdb=" CB THR B 249 " ideal model delta sigma weight residual 1.529 1.487 0.042 1.34e-02 5.57e+03 9.77e+00 bond pdb=" CA TYR A 235 " pdb=" CB TYR A 235 " ideal model delta sigma weight residual 1.525 1.487 0.038 1.47e-02 4.63e+03 6.58e+00 bond pdb=" C LYS B 383 " pdb=" N ASP B 384 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.28e-02 6.10e+03 6.46e+00 bond pdb=" CB PRO D 100 " pdb=" CG PRO D 100 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.63e+00 ... (remaining 12119 not shown) Histogram of bond angle deviations from ideal: 92.28 - 100.67: 17 100.67 - 109.05: 1158 109.05 - 117.44: 7654 117.44 - 125.82: 7467 125.82 - 134.20: 187 Bond angle restraints: 16483 Sorted by residual: angle pdb=" C ASN B 350 " pdb=" N VAL B 351 " pdb=" CA VAL B 351 " ideal model delta sigma weight residual 121.97 133.86 -11.89 1.80e+00 3.09e-01 4.36e+01 angle pdb=" C VAL B 351 " pdb=" N GLU B 352 " pdb=" CA GLU B 352 " ideal model delta sigma weight residual 121.54 132.84 -11.30 1.91e+00 2.74e-01 3.50e+01 angle pdb=" N PHE A 478 " pdb=" CA PHE A 478 " pdb=" C PHE A 478 " ideal model delta sigma weight residual 114.75 107.87 6.88 1.26e+00 6.30e-01 2.99e+01 angle pdb=" N ASN B 168 " pdb=" CA ASN B 168 " pdb=" C ASN B 168 " ideal model delta sigma weight residual 111.87 105.06 6.81 1.41e+00 5.03e-01 2.33e+01 angle pdb=" CA PRO D 100 " pdb=" N PRO D 100 " pdb=" CD PRO D 100 " ideal model delta sigma weight residual 112.00 105.24 6.76 1.40e+00 5.10e-01 2.33e+01 ... (remaining 16478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 6470 18.06 - 36.12: 566 36.12 - 54.18: 90 54.18 - 72.24: 19 72.24 - 90.30: 27 Dihedral angle restraints: 7172 sinusoidal: 2799 harmonic: 4373 Sorted by residual: dihedral pdb=" CA ILE A 519 " pdb=" C ILE A 519 " pdb=" N ASN A 520 " pdb=" CA ASN A 520 " ideal model delta harmonic sigma weight residual 180.00 133.26 46.74 0 5.00e+00 4.00e-02 8.74e+01 dihedral pdb=" CA GLN E 34 " pdb=" C GLN E 34 " pdb=" N GLY E 35 " pdb=" CA GLY E 35 " ideal model delta harmonic sigma weight residual -180.00 -140.36 -39.64 0 5.00e+00 4.00e-02 6.29e+01 dihedral pdb=" CA ALA B 262 " pdb=" C ALA B 262 " pdb=" N TYR B 263 " pdb=" CA TYR B 263 " ideal model delta harmonic sigma weight residual -180.00 -142.86 -37.14 0 5.00e+00 4.00e-02 5.52e+01 ... (remaining 7169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1403 0.062 - 0.124: 357 0.124 - 0.187: 36 0.187 - 0.249: 3 0.249 - 0.311: 1 Chirality restraints: 1800 Sorted by residual: chirality pdb=" CB ILE A 519 " pdb=" CA ILE A 519 " pdb=" CG1 ILE A 519 " pdb=" CG2 ILE A 519 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB THR B 328 " pdb=" CA THR B 328 " pdb=" OG1 THR B 328 " pdb=" CG2 THR B 328 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA TRP A 546 " pdb=" N TRP A 546 " pdb=" C TRP A 546 " pdb=" CB TRP A 546 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1797 not shown) Planarity restraints: 2175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 35 " 0.076 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO B 36 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 107 " -0.021 2.00e-02 2.50e+03 2.39e-02 1.15e+01 pdb=" CG TYR D 107 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR D 107 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR D 107 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 107 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 107 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR D 107 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 107 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 99 " -0.054 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO D 100 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.042 5.00e-02 4.00e+02 ... (remaining 2172 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 100 2.50 - 3.10: 9339 3.10 - 3.70: 17727 3.70 - 4.30: 24830 4.30 - 4.90: 40951 Nonbonded interactions: 92947 Sorted by model distance: nonbonded pdb=" O GLY E 35 " pdb=" O VAL E 76 " model vdw 1.904 3.040 nonbonded pdb=" O GLN D 50 " pdb=" OG1 THR D 53 " model vdw 2.077 2.440 nonbonded pdb=" OH TYR D 110 " pdb=" OD2 ASP D 162 " model vdw 2.151 2.440 nonbonded pdb=" O GLY D 65 " pdb=" OG SER D 68 " model vdw 2.152 2.440 nonbonded pdb=" OG1 THR A 423 " pdb=" OD1 ASP A 447 " model vdw 2.155 2.440 ... (remaining 92942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 2.390 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 31.440 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 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 : 0.007 0.119 12124 Z= 0.474 Angle : 1.045 12.858 16483 Z= 0.631 Chirality : 0.053 0.311 1800 Planarity : 0.007 0.115 2175 Dihedral : 15.004 90.297 4389 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.05 % Favored : 86.75 % Rotamer: Outliers : 0.31 % Allowed : 0.71 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.74 (0.20), residues: 1510 helix: 0.44 (0.27), residues: 334 sheet: -1.73 (0.24), residues: 400 loop : -2.99 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP B 228 HIS 0.008 0.002 HIS A 280 PHE 0.023 0.002 PHE A 490 TYR 0.058 0.003 TYR D 107 ARG 0.022 0.001 ARG D 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 241 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7556 (m-30) cc_final: 0.7324 (m-30) REVERT: A 252 LYS cc_start: 0.7507 (mttt) cc_final: 0.7171 (pttt) REVERT: A 358 ASP cc_start: 0.8395 (m-30) cc_final: 0.8166 (t0) REVERT: A 661 ARG cc_start: 0.6978 (mpp-170) cc_final: 0.6512 (mtm-85) REVERT: A 725 ILE cc_start: 0.3401 (pt) cc_final: 0.3164 (pt) REVERT: A 741 MET cc_start: 0.8623 (ptm) cc_final: 0.8275 (ptt) REVERT: A 777 MET cc_start: 0.7210 (ptm) cc_final: 0.6415 (tpp) REVERT: B 32 MET cc_start: 0.8321 (mpp) cc_final: 0.7955 (mmm) REVERT: B 215 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7510 (tpt90) REVERT: B 392 ARG cc_start: 0.6500 (mpt180) cc_final: 0.5782 (mmt-90) REVERT: C 73 SER cc_start: 0.8015 (p) cc_final: 0.7787 (p) outliers start: 4 outliers final: 1 residues processed: 244 average time/residue: 0.2171 time to fit residues: 77.2385 Evaluate side-chains 199 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN B 172 GLN B 186 ASN B 368 GLN ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12124 Z= 0.214 Angle : 0.739 12.395 16483 Z= 0.394 Chirality : 0.047 0.194 1800 Planarity : 0.005 0.083 2175 Dihedral : 6.976 42.201 1669 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.86 % Favored : 88.87 % Rotamer: Outliers : 1.57 % Allowed : 10.92 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.50 (0.20), residues: 1510 helix: 0.64 (0.27), residues: 345 sheet: -1.57 (0.24), residues: 399 loop : -2.89 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 279 HIS 0.006 0.001 HIS A 280 PHE 0.015 0.001 PHE A 169 TYR 0.025 0.002 TYR D 62 ARG 0.005 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 224 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 THR cc_start: 0.8378 (p) cc_final: 0.8163 (t) REVERT: A 368 GLU cc_start: 0.7023 (tp30) cc_final: 0.6242 (tp30) REVERT: A 373 GLU cc_start: 0.8072 (tt0) cc_final: 0.7861 (tt0) REVERT: A 777 MET cc_start: 0.7030 (ptm) cc_final: 0.6141 (tpp) REVERT: B 63 LEU cc_start: 0.8723 (mp) cc_final: 0.8509 (mt) REVERT: C 73 SER cc_start: 0.7929 (p) cc_final: 0.7728 (p) REVERT: D 79 TYR cc_start: 0.8802 (m-10) cc_final: 0.8438 (m-10) REVERT: D 84 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7754 (p0) outliers start: 20 outliers final: 13 residues processed: 234 average time/residue: 0.2122 time to fit residues: 73.2663 Evaluate side-chains 210 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 121 optimal weight: 0.0050 chunk 135 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12124 Z= 0.180 Angle : 0.688 11.004 16483 Z= 0.364 Chirality : 0.045 0.212 1800 Planarity : 0.005 0.064 2175 Dihedral : 6.431 39.940 1669 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.60 % Favored : 89.21 % Rotamer: Outliers : 1.73 % Allowed : 14.14 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.31 (0.20), residues: 1510 helix: 0.91 (0.27), residues: 346 sheet: -1.42 (0.24), residues: 395 loop : -2.87 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 279 HIS 0.002 0.001 HIS B 165 PHE 0.019 0.001 PHE A 738 TYR 0.047 0.001 TYR D 184 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 217 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.5706 (OUTLIER) cc_final: 0.5249 (pt) REVERT: A 641 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6560 (pp) REVERT: A 719 ILE cc_start: 0.8010 (mp) cc_final: 0.7742 (mp) REVERT: A 777 MET cc_start: 0.6630 (ptm) cc_final: 0.5486 (tpp) REVERT: B 32 MET cc_start: 0.8439 (mpp) cc_final: 0.8074 (mmm) REVERT: D 79 TYR cc_start: 0.8781 (m-10) cc_final: 0.8363 (m-10) REVERT: D 84 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7876 (p0) REVERT: D 223 ARG cc_start: 0.8691 (ttm110) cc_final: 0.8454 (mtp85) outliers start: 22 outliers final: 12 residues processed: 234 average time/residue: 0.2192 time to fit residues: 75.1342 Evaluate side-chains 211 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN B 225 GLN B 302 ASN ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12124 Z= 0.209 Angle : 0.675 11.282 16483 Z= 0.357 Chirality : 0.045 0.262 1800 Planarity : 0.005 0.055 2175 Dihedral : 6.304 40.043 1669 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.06 % Favored : 88.74 % Rotamer: Outliers : 3.14 % Allowed : 14.53 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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 (0.21), residues: 1510 helix: 1.00 (0.27), residues: 347 sheet: -1.39 (0.24), residues: 400 loop : -2.78 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 546 HIS 0.004 0.001 HIS A 280 PHE 0.017 0.001 PHE A 738 TYR 0.031 0.002 TYR D 184 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 202 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLN cc_start: 0.8319 (tp40) cc_final: 0.8100 (tp40) REVERT: A 450 LEU cc_start: 0.5504 (OUTLIER) cc_final: 0.5081 (pp) REVERT: A 549 LEU cc_start: 0.8254 (mm) cc_final: 0.7929 (mm) REVERT: A 641 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6564 (pp) REVERT: A 719 ILE cc_start: 0.8024 (mp) cc_final: 0.7584 (mt) REVERT: A 777 MET cc_start: 0.6596 (ptm) cc_final: 0.5370 (tpt) REVERT: B 85 ASN cc_start: 0.6147 (OUTLIER) cc_final: 0.5934 (p0) REVERT: C 43 GLU cc_start: 0.8714 (mp0) cc_final: 0.7929 (mp0) REVERT: D 84 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7816 (p0) REVERT: D 99 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7788 (p0) outliers start: 40 outliers final: 21 residues processed: 231 average time/residue: 0.2199 time to fit residues: 74.1408 Evaluate side-chains 218 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 0.0570 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 301 GLN ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12124 Z= 0.220 Angle : 0.678 10.710 16483 Z= 0.357 Chirality : 0.045 0.188 1800 Planarity : 0.005 0.048 2175 Dihedral : 6.215 38.952 1669 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.86 % Favored : 88.94 % Rotamer: Outliers : 2.91 % Allowed : 16.58 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.14 (0.21), residues: 1510 helix: 1.07 (0.27), residues: 348 sheet: -1.37 (0.25), residues: 394 loop : -2.74 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 546 HIS 0.003 0.001 HIS A 280 PHE 0.021 0.001 PHE D 64 TYR 0.023 0.001 TYR D 184 ARG 0.004 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLN cc_start: 0.8337 (tp40) cc_final: 0.8120 (tp40) REVERT: A 450 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.5102 (pp) REVERT: A 549 LEU cc_start: 0.8337 (mm) cc_final: 0.7974 (mm) REVERT: A 615 THR cc_start: 0.8364 (m) cc_final: 0.8131 (p) REVERT: A 641 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6564 (pp) REVERT: A 719 ILE cc_start: 0.8029 (mp) cc_final: 0.7602 (mt) REVERT: A 777 MET cc_start: 0.6579 (ptm) cc_final: 0.5306 (tpt) REVERT: B 300 ASP cc_start: 0.7550 (m-30) cc_final: 0.7174 (m-30) REVERT: B 304 ARG cc_start: 0.8250 (ptt-90) cc_final: 0.7837 (ptt-90) REVERT: D 84 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7852 (p0) REVERT: D 99 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7879 (p0) REVERT: D 205 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8410 (p90) REVERT: E 66 ASP cc_start: 0.7990 (t0) cc_final: 0.7739 (t0) outliers start: 37 outliers final: 23 residues processed: 232 average time/residue: 0.2163 time to fit residues: 73.7720 Evaluate side-chains 219 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 145 optimal weight: 0.1980 chunk 120 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 139 optimal weight: 0.9980 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN B 62 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12124 Z= 0.340 Angle : 0.740 10.290 16483 Z= 0.392 Chirality : 0.047 0.222 1800 Planarity : 0.005 0.049 2175 Dihedral : 6.524 40.328 1669 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.72 % Favored : 87.09 % Rotamer: Outliers : 3.06 % Allowed : 17.67 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.17 (0.21), residues: 1510 helix: 0.97 (0.27), residues: 348 sheet: -1.35 (0.25), residues: 392 loop : -2.74 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 206 HIS 0.003 0.001 HIS B 165 PHE 0.021 0.002 PHE A 197 TYR 0.021 0.002 TYR C 41 ARG 0.005 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.7368 (mm110) cc_final: 0.7152 (mm-40) REVERT: A 217 GLN cc_start: 0.8387 (tp40) cc_final: 0.8180 (tp40) REVERT: A 414 VAL cc_start: 0.8985 (t) cc_final: 0.8783 (m) REVERT: A 450 LEU cc_start: 0.5687 (OUTLIER) cc_final: 0.5272 (pp) REVERT: A 549 LEU cc_start: 0.8301 (mm) cc_final: 0.7933 (mm) REVERT: A 641 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6672 (pp) REVERT: A 777 MET cc_start: 0.6761 (ptm) cc_final: 0.5634 (tpt) REVERT: B 121 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.4465 (m90) REVERT: C 43 GLU cc_start: 0.8658 (mp0) cc_final: 0.7946 (mp0) REVERT: D 84 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7853 (p0) REVERT: D 99 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.7945 (p0) REVERT: D 111 MET cc_start: 0.9234 (mmm) cc_final: 0.8936 (tpp) outliers start: 39 outliers final: 30 residues processed: 224 average time/residue: 0.2212 time to fit residues: 72.4834 Evaluate side-chains 224 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 189 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 81 optimal weight: 0.0670 chunk 144 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN B 225 GLN ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12124 Z= 0.217 Angle : 0.698 10.494 16483 Z= 0.366 Chirality : 0.046 0.261 1800 Planarity : 0.005 0.045 2175 Dihedral : 6.254 38.667 1669 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.32 % Favored : 88.48 % Rotamer: Outliers : 2.83 % Allowed : 18.46 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.14 (0.21), residues: 1510 helix: 0.99 (0.27), residues: 350 sheet: -1.30 (0.25), residues: 393 loop : -2.75 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 279 HIS 0.003 0.001 HIS E 83 PHE 0.022 0.001 PHE A 738 TYR 0.022 0.001 TYR D 184 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 198 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5320 (pp) REVERT: A 549 LEU cc_start: 0.8228 (mm) cc_final: 0.7867 (mm) REVERT: A 615 THR cc_start: 0.8429 (m) cc_final: 0.8213 (p) REVERT: A 641 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6580 (pp) REVERT: A 719 ILE cc_start: 0.7942 (mp) cc_final: 0.7574 (mt) REVERT: A 769 SER cc_start: 0.7741 (m) cc_final: 0.7233 (t) REVERT: A 777 MET cc_start: 0.6494 (ptm) cc_final: 0.5324 (tpt) REVERT: B 121 HIS cc_start: 0.6390 (OUTLIER) cc_final: 0.4375 (m90) REVERT: C 43 GLU cc_start: 0.8655 (mp0) cc_final: 0.8006 (mp0) REVERT: D 84 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7843 (p0) REVERT: D 99 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.7887 (p0) outliers start: 36 outliers final: 24 residues processed: 226 average time/residue: 0.2267 time to fit residues: 75.2150 Evaluate side-chains 216 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 91 optimal weight: 0.0980 chunk 98 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12124 Z= 0.177 Angle : 0.682 10.394 16483 Z= 0.356 Chirality : 0.045 0.221 1800 Planarity : 0.004 0.041 2175 Dihedral : 5.990 36.677 1669 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.06 % Favored : 88.74 % Rotamer: Outliers : 2.28 % Allowed : 19.09 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.98 (0.21), residues: 1510 helix: 1.19 (0.27), residues: 346 sheet: -1.19 (0.25), residues: 395 loop : -2.67 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 546 HIS 0.003 0.001 HIS A 280 PHE 0.021 0.001 PHE A 738 TYR 0.024 0.001 TYR D 184 ARG 0.005 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.5582 (OUTLIER) cc_final: 0.4992 (pt) REVERT: A 549 LEU cc_start: 0.8296 (mm) cc_final: 0.7904 (mm) REVERT: A 619 VAL cc_start: 0.8037 (t) cc_final: 0.7644 (m) REVERT: A 641 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6560 (pp) REVERT: A 719 ILE cc_start: 0.7913 (mp) cc_final: 0.7468 (mt) REVERT: A 769 SER cc_start: 0.7544 (m) cc_final: 0.7096 (t) REVERT: A 777 MET cc_start: 0.6321 (ptm) cc_final: 0.5442 (tpt) REVERT: A 789 GLN cc_start: 0.8130 (tp40) cc_final: 0.7821 (mm110) REVERT: B 121 HIS cc_start: 0.6174 (OUTLIER) cc_final: 0.4252 (m90) REVERT: C 43 GLU cc_start: 0.8602 (mp0) cc_final: 0.8053 (mp0) REVERT: D 84 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7707 (p0) REVERT: D 99 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.7936 (p0) REVERT: D 236 LYS cc_start: 0.8347 (ttmm) cc_final: 0.7797 (mtmt) REVERT: E 66 ASP cc_start: 0.7964 (t0) cc_final: 0.7597 (t0) outliers start: 29 outliers final: 22 residues processed: 223 average time/residue: 0.2123 time to fit residues: 70.2583 Evaluate side-chains 217 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 190 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 4.9990 chunk 138 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 0.3980 chunk 41 optimal weight: 0.3980 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 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 217 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12124 Z= 0.177 Angle : 0.685 10.346 16483 Z= 0.354 Chirality : 0.045 0.158 1800 Planarity : 0.004 0.045 2175 Dihedral : 5.863 36.904 1669 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.73 % Favored : 89.07 % Rotamer: Outliers : 2.28 % Allowed : 19.80 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.84 (0.21), residues: 1510 helix: 1.31 (0.27), residues: 346 sheet: -1.07 (0.25), residues: 395 loop : -2.61 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 635 HIS 0.002 0.000 HIS A 280 PHE 0.033 0.001 PHE A 197 TYR 0.021 0.001 TYR D 184 ARG 0.009 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.5461 (OUTLIER) cc_final: 0.4885 (pt) REVERT: A 549 LEU cc_start: 0.8325 (mm) cc_final: 0.7915 (mm) REVERT: A 619 VAL cc_start: 0.8093 (t) cc_final: 0.7730 (m) REVERT: A 641 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6314 (pp) REVERT: A 719 ILE cc_start: 0.7881 (mp) cc_final: 0.7433 (mt) REVERT: A 769 SER cc_start: 0.7519 (m) cc_final: 0.7093 (t) REVERT: A 777 MET cc_start: 0.6285 (ptm) cc_final: 0.5275 (tpt) REVERT: A 789 GLN cc_start: 0.8169 (tp40) cc_final: 0.7826 (mm110) REVERT: B 121 HIS cc_start: 0.6088 (OUTLIER) cc_final: 0.4213 (m90) REVERT: C 43 GLU cc_start: 0.8616 (mp0) cc_final: 0.8113 (mp0) REVERT: C 80 LEU cc_start: 0.8356 (pt) cc_final: 0.8101 (pp) REVERT: D 84 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7669 (p0) REVERT: D 236 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7679 (mtmt) REVERT: E 66 ASP cc_start: 0.7865 (t0) cc_final: 0.7547 (t0) outliers start: 29 outliers final: 22 residues processed: 206 average time/residue: 0.2227 time to fit residues: 67.3173 Evaluate side-chains 210 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN B 225 GLN ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12124 Z= 0.265 Angle : 0.721 10.243 16483 Z= 0.377 Chirality : 0.045 0.155 1800 Planarity : 0.005 0.052 2175 Dihedral : 6.068 37.494 1669 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.19 % Favored : 87.62 % Rotamer: Outliers : 2.44 % Allowed : 19.72 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.90 (0.21), residues: 1510 helix: 1.25 (0.27), residues: 348 sheet: -1.12 (0.25), residues: 390 loop : -2.65 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 546 HIS 0.003 0.001 HIS A 280 PHE 0.036 0.002 PHE A 197 TYR 0.019 0.002 TYR C 41 ARG 0.011 0.001 ARG A 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 ARG cc_start: 0.7444 (mmt180) cc_final: 0.6979 (tpt170) REVERT: A 549 LEU cc_start: 0.8355 (mm) cc_final: 0.7953 (mm) REVERT: A 619 VAL cc_start: 0.7995 (t) cc_final: 0.7758 (m) REVERT: A 641 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6508 (pp) REVERT: A 719 ILE cc_start: 0.8016 (mp) cc_final: 0.7599 (mt) REVERT: A 769 SER cc_start: 0.7771 (m) cc_final: 0.7284 (t) REVERT: A 777 MET cc_start: 0.6386 (ptm) cc_final: 0.5250 (tpt) REVERT: A 789 GLN cc_start: 0.8169 (tp40) cc_final: 0.7822 (mm110) REVERT: B 121 HIS cc_start: 0.6373 (OUTLIER) cc_final: 0.4402 (m90) REVERT: B 360 GLN cc_start: 0.8328 (tp40) cc_final: 0.7988 (tp-100) REVERT: B 392 ARG cc_start: 0.6467 (mpt180) cc_final: 0.5683 (mmt-90) REVERT: C 43 GLU cc_start: 0.8622 (mp0) cc_final: 0.8103 (mp0) REVERT: C 80 LEU cc_start: 0.8438 (pt) cc_final: 0.8200 (pp) REVERT: D 84 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7841 (p0) REVERT: D 99 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.7943 (p0) REVERT: D 236 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7679 (mtmt) REVERT: E 66 ASP cc_start: 0.7966 (t0) cc_final: 0.7688 (t0) outliers start: 31 outliers final: 24 residues processed: 209 average time/residue: 0.2212 time to fit residues: 67.7227 Evaluate side-chains 211 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 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 = 0.4158 r_free = 0.4158 target = 0.182452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.150596 restraints weight = 18178.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149919 restraints weight = 23900.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.151310 restraints weight = 21883.225| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12124 Z= 0.296 Angle : 0.742 10.281 16483 Z= 0.387 Chirality : 0.046 0.157 1800 Planarity : 0.005 0.054 2175 Dihedral : 6.264 38.890 1669 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.65 % Favored : 87.15 % Rotamer: Outliers : 2.51 % Allowed : 20.27 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.02 (0.21), residues: 1510 helix: 1.20 (0.27), residues: 347 sheet: -1.25 (0.25), residues: 392 loop : -2.70 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 546 HIS 0.005 0.001 HIS A 280 PHE 0.033 0.002 PHE A 197 TYR 0.018 0.002 TYR C 41 ARG 0.006 0.001 ARG A 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2354.31 seconds wall clock time: 43 minutes 16.25 seconds (2596.25 seconds total)