Starting phenix.real_space_refine on Tue Feb 13 14:58:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsb_24668/02_2024/7rsb_24668.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsb_24668/02_2024/7rsb_24668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsb_24668/02_2024/7rsb_24668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsb_24668/02_2024/7rsb_24668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsb_24668/02_2024/7rsb_24668.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsb_24668/02_2024/7rsb_24668.pdb" } resolution = 3.68 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= 0.003 sd= 0.033 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 40 5.16 5 C 4362 2.51 5 N 1104 2.21 5 O 1124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A ASP 246": "OD1" <-> "OD2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B GLU 385": "OE1" <-> "OE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6630 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3315 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 423} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3315 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 423} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 4.32, per 1000 atoms: 0.65 Number of scatterers: 6630 At special positions: 0 Unit cell: (72.312, 96.416, 114.232, 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 40 16.00 O 1124 8.00 N 1104 7.00 C 4362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.5 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 76.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 4.405A pdb=" N GLU A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 46 removed outlier: 3.637A pdb=" N LEU A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.984A pdb=" N THR A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 85 removed outlier: 3.686A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 99 removed outlier: 3.554A pdb=" N PHE A 95 " --> pdb=" O MET A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 123 through 140 Proline residue: A 129 - end of helix removed outlier: 3.600A pdb=" N PHE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 167 removed outlier: 4.453A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.724A pdb=" N HIS A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.090A pdb=" N ILE A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 removed outlier: 3.637A pdb=" N ILE A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 251 through 266 removed outlier: 3.844A pdb=" N TYR A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 285 removed outlier: 3.816A pdb=" N ASP A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 removed outlier: 3.589A pdb=" N ALA A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY A 306 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 329 through 349 removed outlier: 3.678A pdb=" N LEU A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 379 removed outlier: 3.523A pdb=" N MET A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.958A pdb=" N ILE A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 392 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 415 removed outlier: 3.709A pdb=" N ILE A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 439 removed outlier: 3.619A pdb=" N ILE A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 removed outlier: 3.674A pdb=" N GLN A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 29 removed outlier: 3.686A pdb=" N GLU B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 59 removed outlier: 3.897A pdb=" N ALA B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 41 " --> pdb=" O PHE B 37 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY B 47 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.566A pdb=" N VAL B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU B 89 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 123 through 140 Proline residue: B 129 - end of helix removed outlier: 3.660A pdb=" N PHE B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 137 " --> pdb=" O PHE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 166 removed outlier: 3.987A pdb=" N THR B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 4.085A pdb=" N ALA B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 removed outlier: 3.763A pdb=" N ILE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.879A pdb=" N GLN B 207 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 233 removed outlier: 3.721A pdb=" N ALA B 217 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET B 228 " --> pdb=" O MET B 224 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 269 Proline residue: B 267 - end of helix Processing helix chain 'B' and resid 270 through 283 removed outlier: 3.698A pdb=" N ASP B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 309 removed outlier: 4.270A pdb=" N MET B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 306 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 329 through 349 removed outlier: 4.017A pdb=" N ILE B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 379 removed outlier: 3.562A pdb=" N ALA B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 removed outlier: 4.120A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 397 " --> pdb=" O GLY B 393 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 398 " --> pdb=" O MET B 394 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 removed outlier: 3.638A pdb=" N ILE B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 439 removed outlier: 3.642A pdb=" N MET B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 460 removed outlier: 3.580A pdb=" N GLN B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 2.79 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: 2067 1.34 - 1.46: 1160 1.46 - 1.57: 3473 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6774 Sorted by residual: bond pdb=" CB ASN B 270 " pdb=" CG ASN B 270 " ideal model delta sigma weight residual 1.516 1.570 -0.054 2.50e-02 1.60e+03 4.59e+00 bond pdb=" CA ASN B 270 " pdb=" CB ASN B 270 " ideal model delta sigma weight residual 1.530 1.566 -0.036 1.69e-02 3.50e+03 4.57e+00 bond pdb=" CA ASN A 270 " pdb=" CB ASN A 270 " ideal model delta sigma weight residual 1.530 1.566 -0.036 1.69e-02 3.50e+03 4.57e+00 bond pdb=" C THR B 31 " pdb=" N PRO B 32 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.44e+00 bond pdb=" CB ASN A 270 " pdb=" CG ASN A 270 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.38e+00 ... (remaining 6769 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.23: 191 106.23 - 113.17: 3589 113.17 - 120.11: 2715 120.11 - 127.06: 2621 127.06 - 134.00: 84 Bond angle restraints: 9200 Sorted by residual: angle pdb=" C PHE B 269 " pdb=" N ASN B 270 " pdb=" CA ASN B 270 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.57e+01 angle pdb=" CA ASN A 270 " pdb=" CB ASN A 270 " pdb=" CG ASN A 270 " ideal model delta sigma weight residual 112.60 117.45 -4.85 1.00e+00 1.00e+00 2.35e+01 angle pdb=" C ASN B 318 " pdb=" N LEU B 319 " pdb=" CA LEU B 319 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" CA ASN B 270 " pdb=" CB ASN B 270 " pdb=" CG ASN B 270 " ideal model delta sigma weight residual 112.60 117.21 -4.61 1.00e+00 1.00e+00 2.13e+01 angle pdb=" CA LEU A 60 " pdb=" CB LEU A 60 " pdb=" CG LEU A 60 " ideal model delta sigma weight residual 116.30 132.32 -16.02 3.50e+00 8.16e-02 2.09e+01 ... (remaining 9195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3471 17.95 - 35.90: 370 35.90 - 53.86: 67 53.86 - 71.81: 9 71.81 - 89.76: 5 Dihedral angle restraints: 3922 sinusoidal: 1476 harmonic: 2446 Sorted by residual: dihedral pdb=" CA SER A 86 " pdb=" C SER A 86 " pdb=" N ALA A 87 " pdb=" CA ALA A 87 " ideal model delta harmonic sigma weight residual 180.00 150.48 29.52 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA GLY A 47 " pdb=" C GLY A 47 " pdb=" N LEU A 48 " pdb=" CA LEU A 48 " ideal model delta harmonic sigma weight residual 180.00 151.78 28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ASN A 270 " pdb=" C ASN A 270 " pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 3919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 742 0.055 - 0.111: 281 0.111 - 0.166: 52 0.166 - 0.222: 7 0.222 - 0.277: 4 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CB VAL B 273 " pdb=" CA VAL B 273 " pdb=" CG1 VAL B 273 " pdb=" CG2 VAL B 273 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE A 356 " pdb=" CA ILE A 356 " pdb=" CG1 ILE A 356 " pdb=" CG2 ILE A 356 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA THR A 31 " pdb=" N THR A 31 " pdb=" C THR A 31 " pdb=" CB THR A 31 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1083 not shown) Planarity restraints: 1154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 266 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.18e+00 pdb=" N PRO B 267 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 149 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO B 150 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 270 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C ASN B 270 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN B 270 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS B 271 " -0.016 2.00e-02 2.50e+03 ... (remaining 1151 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1801 2.80 - 3.32: 6254 3.32 - 3.85: 11297 3.85 - 4.37: 13005 4.37 - 4.90: 22154 Nonbonded interactions: 54511 Sorted by model distance: nonbonded pdb=" OH TYR B 94 " pdb=" OG SER B 350 " model vdw 2.275 2.440 nonbonded pdb=" O ARG A 340 " pdb=" OG1 THR A 344 " model vdw 2.300 2.440 nonbonded pdb=" OH TYR A 94 " pdb=" OG SER A 350 " model vdw 2.301 2.440 nonbonded pdb=" OE2 GLU A 414 " pdb=" OH TYR A 419 " model vdw 2.335 2.440 nonbonded pdb=" O VAL A 412 " pdb=" OG1 THR A 416 " model vdw 2.341 2.440 ... (remaining 54506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.450 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 22.600 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:3.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.006 0.084 6774 Z= 0.428 Angle : 1.069 16.017 9200 Z= 0.549 Chirality : 0.059 0.277 1086 Planarity : 0.008 0.076 1154 Dihedral : 15.190 89.760 2378 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.75 % Allowed : 8.86 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.18 (0.19), residues: 882 helix: -3.05 (0.14), residues: 648 sheet: None (None), residues: 0 loop : -3.92 (0.30), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 291 HIS 0.004 0.001 HIS B 284 PHE 0.019 0.002 PHE A 379 TYR 0.014 0.002 TYR B 210 ARG 0.003 0.000 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 204 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.9328 (mp) cc_final: 0.9101 (mm) REVERT: A 92 PHE cc_start: 0.8744 (t80) cc_final: 0.8525 (t80) REVERT: A 144 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8598 (t) REVERT: A 281 HIS cc_start: 0.7925 (t-90) cc_final: 0.7710 (t-90) REVERT: A 336 ILE cc_start: 0.9010 (mt) cc_final: 0.8729 (mt) REVERT: A 360 MET cc_start: 0.8408 (mtt) cc_final: 0.8163 (mtt) REVERT: B 45 LEU cc_start: 0.8735 (mm) cc_final: 0.8305 (mm) REVERT: B 55 LYS cc_start: 0.8880 (tttt) cc_final: 0.8657 (tttt) REVERT: B 330 MET cc_start: 0.7701 (tpp) cc_final: 0.7112 (ptm) REVERT: B 332 MET cc_start: 0.7835 (tpt) cc_final: 0.7490 (tpp) REVERT: B 455 LYS cc_start: 0.8815 (tmtt) cc_final: 0.8504 (ttpp) outliers start: 5 outliers final: 2 residues processed: 206 average time/residue: 0.2170 time to fit residues: 57.3791 Evaluate side-chains 159 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 156 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 144 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 153 GLN A 157 ASN B 119 GLN B 157 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6774 Z= 0.216 Angle : 0.687 10.056 9200 Z= 0.333 Chirality : 0.042 0.138 1086 Planarity : 0.005 0.058 1154 Dihedral : 5.899 43.593 944 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.45 % Allowed : 17.57 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.24), residues: 882 helix: -1.39 (0.18), residues: 638 sheet: None (None), residues: 0 loop : -3.79 (0.30), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 291 HIS 0.005 0.001 HIS A 284 PHE 0.014 0.001 PHE B 92 TYR 0.014 0.001 TYR A 100 ARG 0.005 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8656 (t) REVERT: A 227 ILE cc_start: 0.9167 (mm) cc_final: 0.8751 (mt) REVERT: A 228 MET cc_start: 0.8187 (mmm) cc_final: 0.7983 (mmm) REVERT: A 243 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7236 (mtpp) REVERT: A 264 ILE cc_start: 0.8692 (pt) cc_final: 0.8437 (pt) REVERT: A 332 MET cc_start: 0.7555 (tpp) cc_final: 0.6678 (tpp) REVERT: A 336 ILE cc_start: 0.9007 (mt) cc_final: 0.8492 (mt) REVERT: B 45 LEU cc_start: 0.8753 (mm) cc_final: 0.8299 (mm) REVERT: B 55 LYS cc_start: 0.8910 (tttt) cc_final: 0.8241 (mtpt) REVERT: B 99 LYS cc_start: 0.7685 (tptt) cc_final: 0.7423 (tptt) REVERT: B 330 MET cc_start: 0.7113 (tpp) cc_final: 0.6618 (ptm) REVERT: B 332 MET cc_start: 0.7679 (tpt) cc_final: 0.7346 (tpp) REVERT: B 403 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.8428 (ttm110) outliers start: 23 outliers final: 11 residues processed: 181 average time/residue: 0.1898 time to fit residues: 45.4170 Evaluate side-chains 158 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 365 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6774 Z= 0.237 Angle : 0.677 10.537 9200 Z= 0.327 Chirality : 0.043 0.209 1086 Planarity : 0.005 0.049 1154 Dihedral : 5.506 46.525 943 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.60 % Allowed : 21.32 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.27), residues: 882 helix: -0.72 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -3.58 (0.31), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 59 HIS 0.013 0.001 HIS A 284 PHE 0.017 0.001 PHE A 92 TYR 0.015 0.002 TYR A 210 ARG 0.004 0.000 ARG B 451 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7801 (t80) cc_final: 0.7600 (t80) REVERT: A 227 ILE cc_start: 0.9187 (mm) cc_final: 0.8753 (mt) REVERT: A 243 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7333 (mtpp) REVERT: A 281 HIS cc_start: 0.8239 (t70) cc_final: 0.7954 (t70) REVERT: A 332 MET cc_start: 0.7510 (tpp) cc_final: 0.7216 (tpp) REVERT: A 336 ILE cc_start: 0.9062 (mt) cc_final: 0.8811 (mt) REVERT: A 397 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8640 (tt) REVERT: B 45 LEU cc_start: 0.8761 (mm) cc_final: 0.8276 (mm) REVERT: B 59 TRP cc_start: 0.8600 (t-100) cc_final: 0.8290 (t-100) REVERT: B 330 MET cc_start: 0.7293 (tpp) cc_final: 0.6422 (ptm) REVERT: B 332 MET cc_start: 0.7662 (tpt) cc_final: 0.7348 (tpp) REVERT: B 403 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.8432 (ttm110) outliers start: 24 outliers final: 18 residues processed: 167 average time/residue: 0.1897 time to fit residues: 41.9923 Evaluate side-chains 163 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 410 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6774 Z= 0.204 Angle : 0.650 10.397 9200 Z= 0.310 Chirality : 0.042 0.156 1086 Planarity : 0.004 0.047 1154 Dihedral : 5.184 45.427 942 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.35 % Allowed : 22.52 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.28), residues: 882 helix: -0.27 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -3.35 (0.31), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 291 HIS 0.013 0.001 HIS B 284 PHE 0.018 0.001 PHE B 92 TYR 0.013 0.001 TYR B 100 ARG 0.003 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8587 (t) REVERT: A 227 ILE cc_start: 0.9157 (mm) cc_final: 0.8752 (mt) REVERT: A 332 MET cc_start: 0.7381 (tpp) cc_final: 0.6773 (tpp) REVERT: A 336 ILE cc_start: 0.9036 (mt) cc_final: 0.8296 (mt) REVERT: A 397 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8571 (tt) REVERT: A 455 LYS cc_start: 0.8716 (ttpp) cc_final: 0.7965 (mtmm) REVERT: B 45 LEU cc_start: 0.8741 (mm) cc_final: 0.8260 (mm) REVERT: B 290 LYS cc_start: 0.8433 (mttm) cc_final: 0.8064 (mttm) REVERT: B 330 MET cc_start: 0.7062 (tpp) cc_final: 0.6363 (ptm) REVERT: B 332 MET cc_start: 0.7656 (tpt) cc_final: 0.7337 (tpp) REVERT: B 403 ARG cc_start: 0.8725 (mmm-85) cc_final: 0.8403 (ttm110) outliers start: 29 outliers final: 18 residues processed: 177 average time/residue: 0.1919 time to fit residues: 44.6973 Evaluate side-chains 164 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 410 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 6774 Z= 0.376 Angle : 0.744 11.009 9200 Z= 0.356 Chirality : 0.046 0.245 1086 Planarity : 0.005 0.062 1154 Dihedral : 5.474 49.482 942 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.50 % Allowed : 23.27 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.28), residues: 882 helix: -0.27 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -3.21 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 59 HIS 0.013 0.002 HIS B 284 PHE 0.013 0.002 PHE A 269 TYR 0.016 0.002 TYR B 100 ARG 0.003 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8815 (t80) cc_final: 0.8454 (t80) REVERT: A 144 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8692 (t) REVERT: A 210 TYR cc_start: 0.7914 (t80) cc_final: 0.7708 (t80) REVERT: A 332 MET cc_start: 0.7533 (tpp) cc_final: 0.7273 (tpp) REVERT: A 336 ILE cc_start: 0.9112 (mt) cc_final: 0.8839 (mt) REVERT: B 45 LEU cc_start: 0.8781 (mm) cc_final: 0.8264 (mm) REVERT: B 74 ASN cc_start: 0.6988 (OUTLIER) cc_final: 0.6108 (p0) REVERT: B 92 PHE cc_start: 0.8978 (t80) cc_final: 0.8775 (t80) REVERT: B 99 LYS cc_start: 0.7950 (tppp) cc_final: 0.7618 (tptt) REVERT: B 216 LYS cc_start: 0.8605 (mttp) cc_final: 0.8377 (mttp) REVERT: B 287 ASN cc_start: 0.8350 (t0) cc_final: 0.7320 (t0) REVERT: B 290 LYS cc_start: 0.8454 (mttm) cc_final: 0.7977 (mmtt) REVERT: B 330 MET cc_start: 0.7410 (tpp) cc_final: 0.6695 (ptt) REVERT: B 332 MET cc_start: 0.7783 (tpt) cc_final: 0.7457 (tpp) outliers start: 30 outliers final: 20 residues processed: 168 average time/residue: 0.1826 time to fit residues: 40.6029 Evaluate side-chains 162 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 0.0970 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 0.0060 chunk 44 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN B 175 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6774 Z= 0.174 Angle : 0.652 10.351 9200 Z= 0.308 Chirality : 0.042 0.181 1086 Planarity : 0.004 0.045 1154 Dihedral : 5.066 45.069 942 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.75 % Allowed : 25.98 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.28), residues: 882 helix: 0.11 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -3.20 (0.32), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 59 HIS 0.011 0.001 HIS B 284 PHE 0.017 0.001 PHE A 379 TYR 0.016 0.001 TYR B 100 ARG 0.002 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8676 (t80) cc_final: 0.8407 (t80) REVERT: A 144 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8564 (t) REVERT: A 210 TYR cc_start: 0.7822 (t80) cc_final: 0.7610 (t80) REVERT: A 227 ILE cc_start: 0.9207 (mm) cc_final: 0.8764 (mt) REVERT: A 332 MET cc_start: 0.7279 (tpp) cc_final: 0.6743 (tpp) REVERT: A 336 ILE cc_start: 0.9023 (mt) cc_final: 0.8304 (mt) REVERT: A 455 LYS cc_start: 0.8683 (ttpp) cc_final: 0.7940 (mtmm) REVERT: B 27 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6360 (mt-10) REVERT: B 45 LEU cc_start: 0.8714 (mm) cc_final: 0.8241 (mm) REVERT: B 208 PHE cc_start: 0.7864 (t80) cc_final: 0.7507 (t80) REVERT: B 290 LYS cc_start: 0.8381 (mttm) cc_final: 0.8105 (mmtp) REVERT: B 330 MET cc_start: 0.7048 (tpp) cc_final: 0.6349 (ptm) REVERT: B 332 MET cc_start: 0.7698 (tpt) cc_final: 0.7382 (tpp) REVERT: B 378 LEU cc_start: 0.8897 (tt) cc_final: 0.8692 (tt) outliers start: 25 outliers final: 18 residues processed: 171 average time/residue: 0.1820 time to fit residues: 41.4172 Evaluate side-chains 159 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 374 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6774 Z= 0.226 Angle : 0.673 10.268 9200 Z= 0.317 Chirality : 0.043 0.167 1086 Planarity : 0.004 0.058 1154 Dihedral : 5.051 45.787 942 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.50 % Allowed : 25.68 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.28), residues: 882 helix: 0.20 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -3.19 (0.33), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 59 HIS 0.014 0.002 HIS B 284 PHE 0.021 0.001 PHE B 92 TYR 0.016 0.002 TYR B 100 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8667 (t80) cc_final: 0.8403 (t80) REVERT: A 144 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8641 (t) REVERT: A 210 TYR cc_start: 0.7842 (t80) cc_final: 0.7513 (t80) REVERT: A 332 MET cc_start: 0.7366 (tpp) cc_final: 0.6790 (tpp) REVERT: A 336 ILE cc_start: 0.9050 (mt) cc_final: 0.8298 (mt) REVERT: A 455 LYS cc_start: 0.8684 (ttpp) cc_final: 0.7946 (mtmm) REVERT: B 45 LEU cc_start: 0.8748 (mm) cc_final: 0.8289 (mm) REVERT: B 55 LYS cc_start: 0.8926 (tttt) cc_final: 0.8273 (mtpt) REVERT: B 99 LYS cc_start: 0.7934 (tppp) cc_final: 0.7572 (tptt) REVERT: B 205 ARG cc_start: 0.7573 (ttp-110) cc_final: 0.7034 (ttp-110) REVERT: B 208 PHE cc_start: 0.7958 (t80) cc_final: 0.7682 (t80) REVERT: B 290 LYS cc_start: 0.8429 (mttm) cc_final: 0.8146 (mmtp) REVERT: B 330 MET cc_start: 0.7155 (tpp) cc_final: 0.6433 (ptt) REVERT: B 332 MET cc_start: 0.7742 (tpt) cc_final: 0.7428 (tpp) REVERT: B 378 LEU cc_start: 0.8906 (tt) cc_final: 0.8692 (tt) outliers start: 30 outliers final: 21 residues processed: 173 average time/residue: 0.1760 time to fit residues: 40.4962 Evaluate side-chains 164 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 291 TRP Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6774 Z= 0.254 Angle : 0.722 11.161 9200 Z= 0.333 Chirality : 0.044 0.232 1086 Planarity : 0.004 0.054 1154 Dihedral : 5.061 45.205 942 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.20 % Allowed : 26.58 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.28), residues: 882 helix: 0.23 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -3.07 (0.33), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 59 HIS 0.013 0.001 HIS B 284 PHE 0.017 0.001 PHE A 379 TYR 0.016 0.001 TYR B 100 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8677 (t80) cc_final: 0.8412 (t80) REVERT: A 144 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8655 (t) REVERT: A 332 MET cc_start: 0.7388 (tpp) cc_final: 0.6799 (tpp) REVERT: A 336 ILE cc_start: 0.9052 (mt) cc_final: 0.8303 (mt) REVERT: A 455 LYS cc_start: 0.8688 (ttpp) cc_final: 0.7948 (mtmm) REVERT: B 45 LEU cc_start: 0.8766 (mm) cc_final: 0.8284 (mm) REVERT: B 55 LYS cc_start: 0.8936 (tttt) cc_final: 0.8281 (mtpt) REVERT: B 99 LYS cc_start: 0.7966 (tppp) cc_final: 0.7580 (tptt) REVERT: B 208 PHE cc_start: 0.7835 (t80) cc_final: 0.7607 (t80) REVERT: B 216 LYS cc_start: 0.8740 (mtmm) cc_final: 0.8506 (mtmm) REVERT: B 290 LYS cc_start: 0.8460 (mttm) cc_final: 0.8184 (mmtp) REVERT: B 330 MET cc_start: 0.7247 (tpp) cc_final: 0.6378 (ptm) REVERT: B 332 MET cc_start: 0.7756 (tpt) cc_final: 0.7439 (tpp) REVERT: B 378 LEU cc_start: 0.8915 (tt) cc_final: 0.8692 (tt) outliers start: 28 outliers final: 23 residues processed: 165 average time/residue: 0.1824 time to fit residues: 40.4418 Evaluate side-chains 170 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 291 TRP Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 435 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6774 Z= 0.207 Angle : 0.704 10.769 9200 Z= 0.323 Chirality : 0.043 0.210 1086 Planarity : 0.004 0.051 1154 Dihedral : 4.956 44.234 942 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.90 % Allowed : 26.73 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.28), residues: 882 helix: 0.34 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -3.08 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 59 HIS 0.012 0.001 HIS B 284 PHE 0.023 0.001 PHE B 92 TYR 0.016 0.002 TYR B 100 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8615 (t80) cc_final: 0.8389 (t80) REVERT: A 144 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8639 (t) REVERT: A 210 TYR cc_start: 0.7990 (t80) cc_final: 0.7681 (t80) REVERT: A 332 MET cc_start: 0.7336 (tpp) cc_final: 0.6807 (tpp) REVERT: A 336 ILE cc_start: 0.9031 (mt) cc_final: 0.8306 (mt) REVERT: A 455 LYS cc_start: 0.8666 (ttpp) cc_final: 0.7914 (mtmm) REVERT: B 45 LEU cc_start: 0.8752 (mm) cc_final: 0.8262 (mm) REVERT: B 55 LYS cc_start: 0.8910 (tttt) cc_final: 0.8276 (mtpt) REVERT: B 209 ARG cc_start: 0.6900 (mtm-85) cc_final: 0.6665 (mpt-90) REVERT: B 290 LYS cc_start: 0.8406 (mttm) cc_final: 0.8170 (mmtp) REVERT: B 330 MET cc_start: 0.7139 (tpp) cc_final: 0.6499 (ptt) REVERT: B 332 MET cc_start: 0.7752 (tpt) cc_final: 0.7430 (tpp) REVERT: B 378 LEU cc_start: 0.8900 (tt) cc_final: 0.8663 (tt) outliers start: 26 outliers final: 21 residues processed: 174 average time/residue: 0.1876 time to fit residues: 43.0025 Evaluate side-chains 163 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 291 TRP Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6774 Z= 0.227 Angle : 0.717 11.050 9200 Z= 0.329 Chirality : 0.043 0.207 1086 Planarity : 0.004 0.048 1154 Dihedral : 4.917 44.273 942 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.45 % Allowed : 26.88 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.28), residues: 882 helix: 0.40 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -3.09 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 59 HIS 0.013 0.001 HIS B 284 PHE 0.018 0.001 PHE A 379 TYR 0.016 0.002 TYR B 100 ARG 0.002 0.000 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8570 (t80) cc_final: 0.8328 (t80) REVERT: A 144 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8640 (t) REVERT: A 210 TYR cc_start: 0.7986 (t80) cc_final: 0.7775 (t80) REVERT: A 332 MET cc_start: 0.7289 (tpp) cc_final: 0.6758 (tpp) REVERT: A 336 ILE cc_start: 0.9034 (mt) cc_final: 0.8307 (mt) REVERT: A 455 LYS cc_start: 0.8664 (ttpp) cc_final: 0.7914 (mtmm) REVERT: B 45 LEU cc_start: 0.8753 (mm) cc_final: 0.8266 (mm) REVERT: B 55 LYS cc_start: 0.8941 (tttt) cc_final: 0.8296 (mtpt) REVERT: B 99 LYS cc_start: 0.7913 (tppp) cc_final: 0.7540 (tptt) REVERT: B 209 ARG cc_start: 0.6807 (mtm-85) cc_final: 0.6548 (mpt-90) REVERT: B 330 MET cc_start: 0.7171 (tpp) cc_final: 0.6457 (ptt) REVERT: B 332 MET cc_start: 0.7742 (tpt) cc_final: 0.7423 (tpp) REVERT: B 338 VAL cc_start: 0.9328 (t) cc_final: 0.9098 (m) REVERT: B 378 LEU cc_start: 0.8888 (tt) cc_final: 0.8658 (tt) outliers start: 23 outliers final: 21 residues processed: 162 average time/residue: 0.1700 time to fit residues: 37.2445 Evaluate side-chains 163 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 291 TRP Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.148520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118126 restraints weight = 9748.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.120945 restraints weight = 6437.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.122854 restraints weight = 5019.543| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6774 Z= 0.210 Angle : 0.716 11.346 9200 Z= 0.329 Chirality : 0.043 0.196 1086 Planarity : 0.004 0.045 1154 Dihedral : 4.867 43.911 942 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.60 % Allowed : 27.63 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.28), residues: 882 helix: 0.52 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -3.11 (0.32), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 59 HIS 0.013 0.001 HIS B 284 PHE 0.024 0.001 PHE B 92 TYR 0.018 0.002 TYR B 419 ARG 0.002 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1584.30 seconds wall clock time: 29 minutes 34.24 seconds (1774.24 seconds total)